Source code for RepTate.tools.ToolIntegral

# RepTate: Rheology of Entangled Polymers: Toolkit for the Analysis of Tool and Experiments
# --------------------------------------------------------------------------------------------------------
#
# Authors:
#     Jorge Ramirez, jorge.ramirez@upm.es
#     Victor Boudara, victor.boudara@gmail.com
#
# Useful links:
#     http://blogs.upm.es/compsoftmatter/software/reptate/
#     https://github.com/jorge-ramirez-upm/RepTate
#     http://reptate.readthedocs.io
#
# --------------------------------------------------------------------------------------------------------
#
# Copyright (2018-2023): Jorge Ramirez, Victor Boudara, Universidad Politécnica de Madrid, University of Leeds
#
# This file is part of RepTate.
#
# RepTate is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# RepTate is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with RepTate.  If not, see <http://www.gnu.org/licenses/>.
#
# --------------------------------------------------------------------------------------------------------
"""Module ToolIntegral

Integral file for creating a new Tool
"""
import traceback
import numpy as np
from RepTate.gui.QTool import QTool
from scipy.integrate import odeint
from scipy.interpolate import interp1d




class ToolIntegral(QTool):
    """Calculate the integral of y with respect to x, where y is the ordinate and x is the abcissa in the current view. Repeated points in the data are removed before the integral is performed. The data between the point is interpolated with a cubic spline. The total value of the definite integral is shown in the Tool output region.
    If a different integration interval is needed, the Bounds tool can be used before the Integral tool.
    """

    toolname = "Integral"
    description = "Integral of current data/view"
    citations = []
    # html_help_file = 'http://reptate.readthedocs.io/manual/Tools/Integral.html'

    def __init__(self, name="", parent_app=None):
        """**Constructor**"""
        super().__init__(name, parent_app)

        # self.function = self.integral  # main Tool function
        # self.parameters['param1'] = Parameter(
        # name='param1',
        # value=1,
        # description='parameter 1',
        # type=ParameterType.real,
        # opt_type=OptType.const)
        self.update_parameter_table()
        self.parent_application.update_all_ds_plots()




    def calculate(self, x, y, ax=None, color=None, file_parameters=[]):
        """Integral function that returns the square of the y, according to the view"""
        xunique, indunique = np.unique(x, return_index=True)
        num_rows = len(xunique)
        yunique = y[indunique]
        try:
            ff = interp1d(
                xunique,
                yunique,
                bounds_error=False,
                kind="cubic",
                fill_value="extrapolate",
                assume_sorted=True,
            )

            func = lambda y0, t: ff(t)
            y2 = odeint(func, [0], xunique)

            y2 = np.reshape(y2, num_rows)
            self.Qprint("<b>I</b> = %g" % y2[-1])
            return xunique, y2
        except Exception as e:
            self.Qprint("in ToolIntegral.calculate(): %s" % traceback.format_exc())
            return x, y