app.py

"""Copyright (c) 2022 VIKTOR B.V.

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
documentation files (the "Software"), to deal in the Software without restriction, including without limitation the
rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit
persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
Software.

VIKTOR B.V. PROVIDES THIS SOFTWARE ON AN "AS IS" BASIS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT
NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF
CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
from pathlib import Path
import numpy as np
import plotly.graph_objects as go
from scipy.integrate import solve_ivp
from viktor.core import ViktorController
from viktor.views import DataGroup
from viktor.views import DataItem
from viktor.views import DataResult
from viktor.views import DataView
from viktor.views import PlotlyResult
from viktor.views import PlotlyView
from viktor.views import WebResult
from viktor.views import WebView

from helper_functions import ode_func
from helper_functions import get_variable_dict
from helper_functions import get_variable_list

from viktor.parametrization import Lookup
from viktor.parametrization import NumberField
from viktor.parametrization import Parametrization
from viktor.parametrization import Section
from viktor.parametrization import Table
from viktor.parametrization import TextField
from viktor.parametrization import ToggleButton


class ODEParametrization(Parametrization):
    """For providing the input fields to users"""
    section_reaction_array = Section('Reaction data')
    section_reaction_array.reactions = Table('reaction data')
    section_reaction_array.reactions.reaction = TextField('Reaction')
    section_reaction_array.reactions.rate_constant = NumberField('Rate constant')

    species_array = Section('Species data')
    species_array.species = Table('Species data')
    species_array.species.name = TextField('Species name')
    species_array.species.concentration = NumberField('Species Concentration')
    species_array.species.matrix = TextField('Applicable reactions')

    time = Section('Time')
    time.begin = NumberField('Begin', default=0)
    time.end = NumberField('End', default=10)
    time.resolution = NumberField('Resolution', default= 10)

    plot_names = Section('Plot names')
    plot_names.toggle = ToggleButton('Change plot names?', default=False)
    plot_names.table = Table('Translations', visible=Lookup('plot_names.toggle'))
    plot_names.table.original = TextField('from')
    plot_names.table.to = TextField('to')


class ODEController(ViktorController):
    """Responsible for visualization and calculation"""

    label = 'ODE'
    parametrization = ODEParametrization

    def execute_ode(self, params):
        """function for solving the differential profiles based on user input"""
        time = [params.time.begin, params.time.end]
        timespan = np.linspace(params.time.begin, params.time.end, params.time.resolution)

        initial_concs = get_variable_list(params.species_array.species, 'concentration')
        applied_reactions = get_variable_list(params.species_array.species, 'matrix')
        reactions = get_variable_list(params.section_reaction_array.reactions, 'reaction')
        names = get_variable_dict(params.species_array.species, 'name')
        constants = get_variable_dict(params.section_reaction_array.reactions, 'rate_constant')

        names = {name['name']: name['index'] for name in names}

        sol = solve_ivp(ode_func, time, initial_concs, t_eval=timespan, args=[constants,
                                                                              reactions,
                                                                              applied_reactions,
                                                                              names])
        return sol

    @DataView('Results numbers', duration_guess=1)
    def get_value_changes(self, params, **kwargs):
        """get the changes at all time points for all species"""
        names = [species['name'] for species in params.species_array.species]

        for replacement in params.plot_names.table:
            i = 0
            for element in names:
                if element == replacement.original:
                    names[i] = replacement.to
                i += 1

        ode_result = self.execute_ode(params)
        runs = []
        i = 0
        for profile in ode_result.y:
            runs.append(DataGroup(DataItem(label=names[i], value=list(profile))))
            i += 1

        result = DataGroup.from_data_groups(runs)

        return DataResult(result)

    @PlotlyView("Plotly view", duration_guess=5)
    def get_progression_plot(self, params, **kwargs):
        """for visualizing all differential profiles in a plot"""
        ode_result = self.execute_ode(params)
        fig = go.Figure()

        names = [species['name'] for species in params.species_array.species]

        for replacement in params.plot_names.table:
            i = 0
            for element in names:
                if element == replacement.original:
                    names[i] = replacement.to
                i += 1

        i = 0
        for profile in ode_result.y:
            fig.add_trace(go.Scatter(x=ode_result.t, y=profile, name=names[i]))
            i += 1

        return PlotlyResult(fig.to_json())
    
    @WebView("What's next?", duration_guess=1)
    def whats_next(self, params, **kwargs):
        """Initiates the process of rendering the "What's next" tab."""
        html_path = Path(__file__).parent / "next_step.html"
        with html_path.open(encoding="utf-8") as _file:
            html_string = _file.read()
        return WebResult(html=html_string)