From 4026533a3f500b4a324c2aa03ebcbafd6de0b1c3 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@alumni.cam.ac.uk>
Date: Tue, 4 Feb 2020 18:15:18 +0000
Subject: [PATCH] add function for reading polynomial files.
---
phasecalculator/io/polynomialio.py | 23 +++++++++++++
.../test/iotest/polynomialiotest.py | 32 ++++++++++++++++++-
2 files changed, 54 insertions(+), 1 deletion(-)
diff --git a/phasecalculator/io/polynomialio.py b/phasecalculator/io/polynomialio.py
index 775cbe0..0d7b2a0 100755
--- a/phasecalculator/io/polynomialio.py
+++ b/phasecalculator/io/polynomialio.py
@@ -21,6 +21,7 @@ Script for running polynomial generation.
"""
import logging
+import solventmapcreator.io.polynomialdatareader as polyread
import solventmapcreator.polynomialanalysis.polynomialplotting as polyplot
logging.basicConfig()
@@ -34,6 +35,28 @@ POSITIVE_POINTS = ["{:.3f}solute".format((float(x)/10.0)) for x in range(101)]
NEGATIVE_POINTS = ["{:.3f}solute".format((float(x)/10.0) - 20.0) for x in range(201)]
+def read_poly_data_to_dict(poly_filename_list, **kwargs):
+ """Parse each file, and then returns the dictionary of information, by solvent ID.
+
+ Parameters
+ ----------
+ poly_filename_list : list
+ list of polynomial file names.
+ suffix : str, optional
+ polynomial file suffix.
+ temperature_dir : bool, optional
+ if files are in temperature based directories, indicates to include
+ the preceding directory name in solvent ID to be able to distiguish
+ the same solvent composition at different temperatures.
+
+ Returns
+ -------
+ dict
+ dict of polynomial data by solvent ID.
+
+ """
+ return polyread.parse_polynomial_data_file_list(poly_filename_list, **kwargs)
+
def generate_polynomial_data_free_energy_file_list(free_energy_filename_list):
"""Generate polynomial fits for free energy data in given files.
diff --git a/phasecalculator/test/iotest/polynomialiotest.py b/phasecalculator/test/iotest/polynomialiotest.py
index 589a67e..b51a143 100755
--- a/phasecalculator/test/iotest/polynomialiotest.py
+++ b/phasecalculator/test/iotest/polynomialiotest.py
@@ -44,6 +44,7 @@ class PolynomialIOTestCase(unittest.TestCase):
None.
"""
+ self.maxDiff = None
parent_directory = pathlib.Path(__file__).parents[1]
self.binding_file = (parent_directory / "resources"/ "expected_parsedbinding.xml").absolute().as_posix()
self.expected_binding_poly = (parent_directory / "resources"/ "expected_bindingpoly.csv").absolute().as_posix()
@@ -63,8 +64,37 @@ class PolynomialIOTestCase(unittest.TestCase):
os.remove(self.actual_binding_poly_file)
if os.path.isfile(self.actual_free_poly_file):
os.remove(self.actual_free_poly_file)
+ def test_read_poly_data_to_dict(self):
+ """Test expected_polynomial information read in.
+
+ Returns
+ -------
+ None.
+
+ """
+ expected_dict = {'resourcesexpected,parsed':{8: {'negative': {'RMSE': 0.0137444779,
+ 'coefficients': np.array([-2.60836624e-01, 4.65295250e-01, 2.57637417e-01, 2.19491128e-01,
+ 4.20087475e-02, 4.02289353e-03, 2.12247938e-04, 5.89243946e-06,
+ 6.73443996e-08]),
+ 'covar': 0.0379710451935,
+ 'order': 8},
+ 'positive': {'RMSE': 0.008907316,
+ 'coefficients': np.array([-2.52075337e-01, -7.07009850e-01, 9.86359325e-01, -1.40859321e+00,
+ 5.04060101e-01, -9.17970326e-02, 9.28812463e-03, -4.97458825e-04,
+ 1.10198937e-05]),
+ 'covar': 0.008013368123414,
+ 'order': 8}}}}
+ actual_dict = polyio.read_poly_data_to_dict([self.expected_free_poly], suffix="freepoly.csv",
+ temperature_dir=True)
+ self.assertListEqual(list(expected_dict.keys()), list(actual_dict.keys()))
+ for region, info_dict in actual_dict['resourcesexpected,parsed'][8].items():
+ for key, value in info_dict.items():
+ if key == "coefficients":
+ np.testing.assert_allclose(value, expected_dict['resourcesexpected,parsed'][8][region][key])
+ else:
+ self.assertEqual(value, expected_dict['resourcesexpected,parsed'][8][region][key])
def test_generate_polynomial_data_free_energy_file_list(self):
- """Test expected polynomial data ouputed.
+ """Test expected polynomial data outputed.
Returns
-------
--
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