From 33fc558de5c23b7406189c1a6b5eabd9108c268a Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@cam.ac.uk>
Date: Wed, 5 Jul 2017 23:01:57 +0100
Subject: [PATCH] created script for writing out the polynomial fit
information, and corresponding tests.
---
solventmapcreator/io/polynomialdatawriter.py | 41 +++++++
.../test/iotest/polynomialdatawritertest.py | 104 ++++++++++++++++++
.../test/resources/expected_poly_fit.csv | 2 +
.../test/solvationmapcreatortests.py | 3 +-
4 files changed, 149 insertions(+), 1 deletion(-)
create mode 100644 solventmapcreator/io/polynomialdatawriter.py
create mode 100644 solventmapcreator/test/iotest/polynomialdatawritertest.py
create mode 100644 solventmapcreator/test/resources/expected_poly_fit.csv
diff --git a/solventmapcreator/io/polynomialdatawriter.py b/solventmapcreator/io/polynomialdatawriter.py
new file mode 100644
index 0000000..b690b61
--- /dev/null
+++ b/solventmapcreator/io/polynomialdatawriter.py
@@ -0,0 +1,41 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script for generating the polynomial fit information and writing to file.
+
+@author: mark
+"""
+
+import logging
+import resultsanalysis.resultsoutput.resultswritertofile as resultswritertofile
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+def write_poly_data_to_file(datapoints, order_list, filename):
+ """This calculates the polynomial information, and then outputs the
+ information to file.
+ """
+ poly_fit_data = generate_poly_fit_data_order_list(datapoints, order_list)
+ return write_poly_fit_data_to_file(poly_fit_data, filename)
+
+def write_poly_fit_data_to_file(poly_fit_data, filename):
+ """This writes the information to file.
+ """
+ return resultswritertofile.write_poly_fit_information_to_file(poly_fit_data, filename)
+
+def generate_poly_fit_data_order_list(datapoints, order_list):
+ """This cretes the polynomial fit data for all the given polynomial orders
+ for the datapoints given
+ """
+ poly_fit_data = {}
+ for order in order_list:
+ poly_fit_data[order] = generate_polynomial_fit_data(datapoints, order)
+ return poly_fit_data
+
+def generate_polynomial_fit_data(datapoints, order):
+ """This creates the polynomial fit data for the given order of polynomial
+ for the datapoints given.
+ """
+ return datapoints.poly_fit_data(order)
diff --git a/solventmapcreator/test/iotest/polynomialdatawritertest.py b/solventmapcreator/test/iotest/polynomialdatawritertest.py
new file mode 100644
index 0000000..37c44a6
--- /dev/null
+++ b/solventmapcreator/test/iotest/polynomialdatawritertest.py
@@ -0,0 +1,104 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Script for testingthe polynomialdatawriter script.
+
+@author: mark
+"""
+
+import logging
+import unittest
+import numpy as np
+import os
+from resultsanalysis.dataclasses.datapoint import Datapoint
+from resultsanalysis.dataclasses.units import Units
+from resultsanalysis.dataclasses.value import Value
+import resultsanalysis.dataclasses.datapoints as Datapoints
+import solventmapcreator.io.polynomialdatawriter as polynomialdatawriter
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+class PolynomialDataWriterTestCase(unittest.TestCase):
+ """Test case for the polynomial data writer.
+ """
+ def setUp(self):
+ """Set up for test cases
+ """
+ self.datapoints = Datapoints.Datapoints(('Log(Sw)', 'Log(Sw)'),
+ (Units.dimensionless, Units.dimensionless))
+ self.datapoints.addDatapointList([Datapoint(Value(1.0, 'Log(Sw)', Units.dimensionless),
+ Value(1.0, 'Log(Sw)', Units.dimensionless), 'EXAMPLE1'),
+ Datapoint(Value(2.0, 'Log(Sw)', Units.dimensionless),
+ Value(2.1, 'Log(Sw)', Units.dimensionless), 'EXAMPLE2'),
+ Datapoint(Value(0.5, 'Log(Sw)', Units.dimensionless),
+ Value(0.5, 'Log(Sw)', Units.dimensionless), 'EXAMPLE3')])
+ self.datapoints.createDataArrays()
+ self.expected_polynomial_data = {1:{"coefficients":np.array([-0.05,
+ 1.07142857]),
+ "RMSE":0.015430334996209221,
+ "order":1,
+ "covar":np.array([0.0007143])}}
+ self.expected_file_name = "resources/expected_poly_fit.csv"
+ def tearDown(self):
+ """Tear down after tests
+ """
+ del self.datapoints
+ del self.expected_polynomial_data
+ del self.expected_file_name
+ if os.path.isfile("actual_poly_fit.csv"):
+ os.remove("actual_poly_fit.csv")
+ def test_write_poly_data_to_file(self):
+ """Test to see if expected file is produced.
+ """
+ actual_file_name = "actual_poly_fit.csv"
+ poly_file_out = polynomialdatawriter.write_poly_data_to_file(self.datapoints,
+ [1], actual_file_name)
+ self.assertEqual(0, poly_file_out)
+ with open(self.expected_file_name, 'r') as exp_file:
+ exp_file_lines = exp_file.readlines()
+ with open(actual_file_name, 'r') as act_file:
+ act_file_lines = act_file.readlines()
+ self.assertListEqual(act_file_lines, exp_file_lines)
+ def test_write_poly_fit_data_to_file(self):
+ """Test to see if expected file is produced.
+ """
+ actual_file_name = "actual_poly_fit.csv"
+ poly_file_out = polynomialdatawriter.write_poly_fit_data_to_file(self.expected_polynomial_data,
+ actual_file_name)
+ self.assertEqual(0, poly_file_out)
+ with open(self.expected_file_name, 'r') as exp_file:
+ exp_file_lines = exp_file.readlines()
+ with open(actual_file_name, 'r') as act_file:
+ act_file_lines = act_file.readlines()
+ self.assertListEqual(act_file_lines, exp_file_lines)
+ def test_generate_poly_fit_data_order_list(self):
+ """Test to see if expected dictionary is produced.
+ """
+ actual_poly_dictionary = polynomialdatawriter.generate_poly_fit_data_order_list(self.datapoints, [1])
+ self.assertListEqual(sorted(self.expected_polynomial_data.keys()), sorted(actual_poly_dictionary.keys()))
+ for poly_order in self.expected_polynomial_data.keys():
+ expected_dictionary = self.expected_polynomial_data[poly_order]
+ actual_dictionary = actual_poly_dictionary[poly_order]
+ for key in expected_dictionary.keys():
+ if key == "RMSE":
+ 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_polynomial_fit_data(self):
+ """Test to see if expected dictionary is produced.
+ """
+ actual_dictionary = polynomialdatawriter.generate_polynomial_fit_data(self.datapoints, 1)
+ expected_dictionary = self.expected_polynomial_data[1]
+ self.assertListEqual(sorted(expected_dictionary.keys()), sorted(actual_dictionary.keys()))
+ for key in expected_dictionary.keys():
+ if key == "RMSE":
+ 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])
+
diff --git a/solventmapcreator/test/resources/expected_poly_fit.csv b/solventmapcreator/test/resources/expected_poly_fit.csv
new file mode 100644
index 0000000..6a37847
--- /dev/null
+++ b/solventmapcreator/test/resources/expected_poly_fit.csv
@@ -0,0 +1,2 @@
+Order RMSE Covariance Coefficients
+1 0.0154303 0.0007143 -0.0500000 1.0714286
diff --git a/solventmapcreator/test/solvationmapcreatortests.py b/solventmapcreator/test/solvationmapcreatortests.py
index 151dbdc..da27e68 100644
--- a/solventmapcreator/test/solvationmapcreatortests.py
+++ b/solventmapcreator/test/solvationmapcreatortests.py
@@ -9,13 +9,14 @@ Script for running the tests.
import logging
import unittest
from solventmapcreator.test.iotest.solvationenergyreadertest import SolvationEnergyReaderTestCase
+from solventmapcreator.test.iotest.polynomialdatawritertest import PolynomialDataWriterTestCase
from solventmapcreator.test.solvationcalculationtest.solvationcalculatortest import SolvationCalculatorTestCase
logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
-IO_TEST_CASES = [SolvationEnergyReaderTestCase]
+IO_TEST_CASES = [SolvationEnergyReaderTestCase, PolynomialDataWriterTestCase]
SOLVATION_CALCULATION_TEST_CASES = [SolvationCalculatorTestCase]
def test_suite():
--
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