From 839055053b3032f7b0ba19ba7517cb308c15d081 Mon Sep 17 00:00:00 2001
From: Mark Driver <mdd31@cam.ac.uk>
Date: Sat, 12 Aug 2017 18:23:46 +0100
Subject: [PATCH] added functionality to plot using split polynomials.
---
.../polynomialanalysis/polynomialplotting.py | 48 ++++++++++++++++--
.../polynomialplottingtest.py | 49 +++++++++++++++++++
2 files changed, 93 insertions(+), 4 deletions(-)
diff --git a/solventmapcreator/polynomialanalysis/polynomialplotting.py b/solventmapcreator/polynomialanalysis/polynomialplotting.py
index 083144f..0a24f81 100644
--- a/solventmapcreator/polynomialanalysis/polynomialplotting.py
+++ b/solventmapcreator/polynomialanalysis/polynomialplotting.py
@@ -8,6 +8,8 @@ the polynomial fit data and also the plots.
"""
import logging
+import numpy as np
+import solventmapcreator.polynomialanalysis.polynomialvaluecalculator as polyvalcalc
import resultsanalysis.resultsoutput.plottinginput as plottinginput
import solventmapcreator.io.polynomialdatawriter as polynomialdatawriter
import solventmapcreator.io.solvationenergyreader as solvationenergyreader
@@ -16,21 +18,59 @@ logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
-def plot_energies_from_file(free_energy_filename, polynomial_order):
+def plot_energies_from_file(free_energy_filename, polynomial_order, **kwargs):
"""This creates in the plotting information, and outputs a plot to file.
+ """
+ plot_data = parse_energies_create_plot_input_data(free_energy_filename,
+ polynomial_order,
+ kwargs.get("pos_subset_list", None),
+ kwargs.get("neg_subset_list", None))
+ if type(plot_data['polynomial coefficients']) is dict:
+ return create_scatter_with_split_poly(plot_data, **kwargs)
+ else:
+ return plottinginput.create_scatter_graph_with_polynomial(plot_data)
+
+def create_scatter_with_split_poly(input_data, **kwargs):
+ """This generates the split plot when a split polynomial is required.
"""
- plot_data = parse_energies_create_plot_input_data(free_energy_filename, polynomial_order)
- return plottinginput.create_scatter_graph_with_polynomial(plot_data)
+ scatter_plot, scatter_plot_axis = plottinginput.plot_scatter_graph(input_data)
+ x_data = np.sort(input_data['x_data'])
+ polynomial_values = polyvalcalc.calculate_polynomial_values(x_data,
+ input_data["polynomial coefficients"])
+ plottinginput.plot_polynomial_curve(scatter_plot_axis, x_data,
+ polynomial_values,
+ input_data["polynomial order"])
+ fileformat = kwargs.get("fileformat", "eps")
+ output_filename = plottinginput.create_output_filename(input_data, fileformat)
+ plottinginput.plt.savefig(output_filename, format=fileformat)
+ plottinginput.plt.close(scatter_plot)
+ return 0
-def parse_energies_create_plot_input_data(free_energy_filename, polynomial_order):
+def parse_energies_create_plot_input_data(free_energy_filename, polynomial_order,
+ pos_subset_list=None, neg_subset_list=None):
"""This creates the input data for a plot. This overrides the default figure
label, so that the figures can be distinguished based on the solvent.
"""
datapoints = parse_free_energy_from_file_with_data_arrays(free_energy_filename)
plot_data = datapoints.generateScatterPlotParameters(label_type='', polynomial_order=polynomial_order)
+ if pos_subset_list != None and neg_subset_list != None:
+ poly_coeff_dict = generate_poly_pos_neg_separate_fit(datapoints, polynomial_order,
+ pos_subset_list, neg_subset_list)
+ plot_data['polynomial coefficients'] = poly_coeff_dict
plot_data['figure_label'] = free_energy_filename.replace('.xml', '')
return plot_data
+def generate_poly_pos_neg_separate_fit(datapoints, order, pos_subset_list, neg_subset_list):
+ """This generates the fit for the positive and negative datapoints separately.
+ A dictionary containing the 2 fits are returned.
+ """
+ poly_dict = polynomialdatawriter.generate_polynomial_fit_data_positive_negative_separate_fit(datapoints,
+ order,
+ pos_subset_list,
+ neg_subset_list)
+ return {"positive":poly_dict["positive"]["coefficients"],
+ "negative":poly_dict["negative"]["coefficients"]}
+
def parse_poly_data_to_file_split_fit(free_energy_filename, order_list, poly_filename,
pos_subset_list, neg_subset_list):
"""This reads in the energy information, and then performs the fits on the
diff --git a/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py b/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py
index 1a2a210..70c65a4 100644
--- a/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py
+++ b/solventmapcreator/test/polynomialanalysistest/polynomialplottingtest.py
@@ -73,6 +73,55 @@ class PolynomialPlottingTestCase(unittest.TestCase):
else:
LOGGER.debug("assert equal string")
self.assertEqual(actual_dict[key], expected_dict[key])
+ #test to see if new functionality is supported
+ neg_set_list = ["-5.400solute", "-4.300solute", "-9.100solute", "-11.100solute", "-15.400solute"]
+ pos_set_list = ["0.500solute", "1.200solute", "7.200solute"]
+ actual_dict2 = polynomialplotting.parse_energies_create_plot_input_data("resources/water.xml", 4,
+ pos_set_list, neg_set_list)
+ self.assertListEqual(sorted(actual_dict2.keys()), sorted(expected_dict.keys()))
+ for key in actual_dict.keys():
+ LOGGER.debug("Key: %s", key)
+ if key == 'y_data' or key == 'x_data':
+ LOGGER.debug("assert equal array x and y data")
+ np.testing.assert_array_almost_equal(actual_dict2[key],
+ expected_dict[key])
+ elif key == 'polynomial coefficients':
+ self.assertListEqual(["negative", "positive"],
+ sorted(actual_dict2['polynomial coefficients'].keys()))
+ negative_coeffs = np.array([5.038843e+00, 2.290628e+00, -9.855830e-02,
+ -6.480660e-03, -1.545673e-04])
+ positive_coeffs = np.array([1.351575, -1.317976, -0.126786,
+ -0.015156, -0.002038])
+ np.testing.assert_array_almost_equal(negative_coeffs,
+ actual_dict2['polynomial coefficients']["negative"])
+ np.testing.assert_array_almost_equal(positive_coeffs,
+ actual_dict2['polynomial coefficients']["positive"])
+ elif key == 'plot_axis_range' or key == 'x_axis_range' or key == 'y_axis_range':
+ np.testing.assert_array_almost_equal(np.array(actual_dict2[key]),
+ np.array(expected_dict[key]))
+ else:
+ LOGGER.debug("assert equal string")
+ self.assertEqual(actual_dict2[key], expected_dict[key])
+ def test_generate_poly_pos_neg_separate_fit(self):
+ """Test to see if expected dict is returned.
+ """
+
+ neg_set_list = ["-5.400solute", "-4.300solute", "-9.100solute", "-11.100solute", "-15.400solute"]
+ pos_set_list = ["0.500solute", "1.200solute", "7.200solute"]
+ negative_coeffs = np.array([5.038843e+00, 2.290628e+00, -9.855830e-02,
+ -6.480660e-03, -1.545673e-04])
+ positive_coeffs = np.array([1.351575, -1.317976, -0.126786, -0.015156,
+ -0.002038])
+ actual_dict = polynomialplotting.generate_poly_pos_neg_separate_fit(self.expected_datapoints, 4,
+ pos_set_list, neg_set_list)
+ LOGGER.debug("Actual Dict")
+ LOGGER.debug(actual_dict)
+ self.assertListEqual(["negative", "positive"],
+ sorted(actual_dict.keys()))
+ np.testing.assert_array_almost_equal(negative_coeffs,
+ actual_dict["negative"])
+ np.testing.assert_array_almost_equal(positive_coeffs,
+ actual_dict["positive"])
def test_parse_poly_data_to_file_split_fit(self):
"""Test to see if expected fit is done on the positive and negative subsets
after the file was read in.
--
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