From d18ceba124752a4c1aa287c35d419477430fd87c Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@cam.ac.uk>
Date: Thu, 6 Jul 2017 16:11:13 +0100
Subject: [PATCH] added script containing methods for reading in polynomial fit
data.
---
solventmapcreator/io/polynomialdatareader.py | 65 +++++++++++++
.../test/iotest/polynomialdatareadertest.py | 95 +++++++++++++++++++
.../test/solvationmapcreatortests.py | 4 +-
3 files changed, 163 insertions(+), 1 deletion(-)
create mode 100644 solventmapcreator/io/polynomialdatareader.py
create mode 100644 solventmapcreator/test/iotest/polynomialdatareadertest.py
diff --git a/solventmapcreator/io/polynomialdatareader.py b/solventmapcreator/io/polynomialdatareader.py
new file mode 100644
index 0000000..e51e8c9
--- /dev/null
+++ b/solventmapcreator/io/polynomialdatareader.py
@@ -0,0 +1,65 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script for reading in polynomial data from the csv files.
+
+@author: mark
+"""
+
+import logging
+import numpy as np
+import csv
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+def parse_polynomial_data_file_list(filename_list):
+ """This parses each file, and then returns the dictionary containing the
+ information, by solvent ID.
+ """
+ polynomial_data_by_solventid ={}
+ for filename in filename_list:
+ solvent_id = generate_solvent_id(filename)
+ polynomial_fit_data = parse_polynomial_data_file(filename)
+ polynomial_data_by_solventid[solvent_id] = polynomial_fit_data
+ return polynomial_data_by_solventid
+
+def generate_solvent_id(filename):
+ """This gets the solvent ID from the filename. assumes file name is of the
+ form '*/solventID.csv' where 'solventID' is the solvent ID.
+ """
+ return filename.split('/')[-1].replace('.csv', '')
+
+def parse_polynomial_data_file(filename):
+ """This reads in the file and parses the polynomial lines.
+ """
+ polynomial_data_dict = {}
+ data_in = read_polynomial_data_file(filename)
+ for line_list in data_in[1:]:
+ polynomial_data = read_polynomial_data_line(line_list)
+ polynomial_data_dict[polynomial_data["order"]] = polynomial_data
+ return polynomial_data_dict
+
+def read_polynomial_data_file(filename):
+ """This reads in the tab separated variable file containing the polynomial fit data.
+ """
+ data_in = []
+ with open(filename, "r") as file_in:
+ file_contents = csv.reader(file_in, delimiter='\t')
+ for line in file_contents:
+ data_in.append(line)
+ return data_in
+
+def read_polynomial_data_line(line_list):
+ """This reads in the values to a dictionary.
+ This assumes that the values in the line are formatted such that they are
+ ordered:
+ Order, RMSE, covariance, coefficients.
+ """
+ order = int(line_list[0])
+ RMSE = float(line_list[1])
+ covariance = float(line_list[2])
+ coefficients = np.array([float(x) for x in line_list[3:]])
+ return {"order": order, "RMSE":RMSE, "covar":covariance,
+ "coefficients":coefficients}
diff --git a/solventmapcreator/test/iotest/polynomialdatareadertest.py b/solventmapcreator/test/iotest/polynomialdatareadertest.py
new file mode 100644
index 0000000..cf39aea
--- /dev/null
+++ b/solventmapcreator/test/iotest/polynomialdatareadertest.py
@@ -0,0 +1,95 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script for testing the polynomialdatareader script.
+
+@author: mark
+"""
+
+import logging
+import unittest
+import numpy as np
+import solventmapcreator.io.polynomialdatareader as polynomialdatareader
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+class PolynomialDataReaderTestCase(unittest.TestCase):
+ """Test Case for the polynomialdatareader script.
+ """
+ def setUp(self):
+ """Set up for tests.
+ """
+ self.expected_list = [['Order', 'RMSE', 'Covariance', 'Coefficients'],
+ ['1', '0.0154303', '0.0007143', '-0.0500000', '1.0714286']]
+ self.expected_data_by_solvent_id = {"expected_poly_fit":{1:{"coefficients":np.array([-0.05,
+ 1.07142857]),
+ "RMSE":0.015430334996209221,
+ "order":1,
+ "covar":0.0007143}}}
+ def tearDown(self):
+ """Tear down after tests.
+ """
+ del self.expected_data_by_solvent_id
+ del self.expected_list
+ def test_parse_polynomial_data_file_list(self):
+ """Test to see if expected information is read in from file list.
+ """
+ actual_data_by_solvent_id = polynomialdatareader.parse_polynomial_data_file_list(["resources/expected_poly_fit.csv"])
+ self.assertListEqual(sorted(self.expected_data_by_solvent_id.keys()), sorted(actual_data_by_solvent_id.keys()))
+ expected_poly_dictionary = self.expected_data_by_solvent_id["expected_poly_fit"]
+ actual_poly_dictionary = actual_data_by_solvent_id["expected_poly_fit"]
+ self.assertListEqual(sorted(expected_poly_dictionary.keys()), sorted(actual_poly_dictionary.keys()))
+ for poly_order in expected_poly_dictionary.keys():
+ expected_dictionary = expected_poly_dictionary[poly_order]
+ actual_dictionary = actual_poly_dictionary[poly_order]
+ for key in expected_dictionary.keys():
+ if key == "RMSE" or key == "covar":
+ self.assertAlmostEqual(expected_dictionary[key], actual_dictionary[key])
+ elif key == "order":
+ self.assertEqual(expected_dictionary[key], actual_dictionary[key])
+ else:
+ np.testing.assert_array_almost_equal(expected_dictionary[key], actual_dictionary[key])
+ def test_generate_solvent_id(self):
+ """Test to see if expected id is extracted.
+ """
+ expected_id = "water"
+ actual_id1 = polynomialdatareader.generate_solvent_id("water.csv")
+ self.assertEqual(expected_id, actual_id1)
+ actual_id2 = polynomialdatareader.generate_solvent_id("resources/water.csv")
+ self.assertEqual(expected_id, actual_id2)
+ def test_parse_polynomial_data_file(self):
+ """Test to see if file is parsed as expected.
+ """
+ expected_poly_dictionary = self.expected_data_by_solvent_id["expected_poly_fit"]
+ actual_poly_dictionary = polynomialdatareader.parse_polynomial_data_file("resources/expected_poly_fit.csv")
+ self.assertListEqual(sorted(expected_poly_dictionary.keys()), sorted(actual_poly_dictionary.keys()))
+ for poly_order in expected_poly_dictionary.keys():
+ expected_dictionary = expected_poly_dictionary[poly_order]
+ actual_dictionary = actual_poly_dictionary[poly_order]
+ for key in expected_dictionary.keys():
+ if key == "RMSE" or key == "covar":
+ self.assertAlmostEqual(expected_dictionary[key], actual_dictionary[key])
+ elif key == "order":
+ self.assertEqual(expected_dictionary[key], actual_dictionary[key])
+ else:
+ np.testing.assert_array_almost_equal(expected_dictionary[key], actual_dictionary[key])
+ def test_read_polynomial_data_file(self):
+ """Test to see if file is read as expected.
+ """
+ actual_list = polynomialdatareader.read_polynomial_data_file("resources/expected_poly_fit.csv")
+ self.assertListEqual(self.expected_list, actual_list)
+ def test_read_polynomial_data_line(self):
+ """Test to see if line is read as expected.
+ """
+ expected_dictionary = self.expected_data_by_solvent_id["expected_poly_fit"][1]
+ actual_dictionary = polynomialdatareader.read_polynomial_data_line(self.expected_list[1])
+ self.assertListEqual(sorted(expected_dictionary.keys()), sorted(actual_dictionary.keys()))
+ for key in expected_dictionary.keys():
+ if key == "RMSE" or key == "covar":
+ self.assertAlmostEqual(expected_dictionary[key], actual_dictionary[key])
+ elif key == "order":
+ self.assertEqual(expected_dictionary[key], actual_dictionary[key])
+ else:
+ np.testing.assert_array_almost_equal(expected_dictionary[key], actual_dictionary[key])
\ No newline at end of file
diff --git a/solventmapcreator/test/solvationmapcreatortests.py b/solventmapcreator/test/solvationmapcreatortests.py
index da27e68..a251085 100644
--- a/solventmapcreator/test/solvationmapcreatortests.py
+++ b/solventmapcreator/test/solvationmapcreatortests.py
@@ -10,13 +10,15 @@ import logging
import unittest
from solventmapcreator.test.iotest.solvationenergyreadertest import SolvationEnergyReaderTestCase
from solventmapcreator.test.iotest.polynomialdatawritertest import PolynomialDataWriterTestCase
+from solventmapcreator.test.iotest.polynomialdatareadertest import PolynomialDataReaderTestCase
from solventmapcreator.test.solvationcalculationtest.solvationcalculatortest import SolvationCalculatorTestCase
logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
-IO_TEST_CASES = [SolvationEnergyReaderTestCase, PolynomialDataWriterTestCase]
+IO_TEST_CASES = [SolvationEnergyReaderTestCase, PolynomialDataWriterTestCase,
+ PolynomialDataReaderTestCase]
SOLVATION_CALCULATION_TEST_CASES = [SolvationCalculatorTestCase]
def test_suite():
--
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