AdisTS.py

# AdisTS.py -- Pamhyr
# Copyright (C) 2023-2024  INRAE
#
# This program 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.
#
# This program 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 this program.  If not, see <https://www.gnu.org/licenses/>.

# -*- coding: utf-8 -*-

import os, glob
import logging
from http.cookiejar import reach

import numpy as np

import shutil

from tools import (
    trace, timer, logger_exception,
    timestamp_to_old_pamhyr_date,
    old_pamhyr_date_to_timestamp,
    timestamp_to_old_pamhyr_date_adists
)

from Solver.CommandLine import CommandLineSolver

from Model.Results.Results import Results
from Model.Results.River.River import River, Reach, Profile

from Checker.Adists import (
    AdistsOutputKpChecker,
)

logger = logging.getLogger()

def adists_file_open(filepath, mode):
    f = open(filepath, mode)

    if "w" in mode:
        # Write header
        comment = "*"
        if ".ST" in filepath:
            comment = "#"

        f.write(
            f"{comment} " +
            "This file is generated by PAMHYR, please don't modify\n"
        )

    return f

class AdisTS(CommandLineSolver):
    _type = "adists"

    def __init__(self, name):
        super(AdisTS, self).__init__(name)

        self._type = "adists"

        self._cmd_input = ""
        self._cmd_solver = "@path @input -o @output"
        self._cmd_output = ""

    @classmethod
    def default_parameters(cls):
        lst = super(AdisTS, cls).default_parameters()

        lst += [
            ("adists_implicitation_parameter", "0.5"),
            ("adists_timestep_screen", "60"),
            ("adists_timestep_bin", "60"),
            ("adists_timestep_csv", "60"),
            ("adists_timestep_mage", "60"),
            ("adists_initial_concentration", "60"),
        ]

        return lst

    @classmethod
    def checkers(cls):
        lst = [
            AdistsOutputKpChecker(),
        ]

        return lst

    def cmd_args(self, study):
        lst = super(AdisTS, self).cmd_args(study)
        return lst

    def input_param(self):
        name = self._study.name
        return f"{name}.REP"

    def log_file(self):
        name = self._study.name
        return f"{name}.TRA"

    def _export_REP_additional_lines(self, study, rep_file):
        lines = filter(
            lambda line: line.is_enabled(),
            study.river.rep_lines.lines
        )

        for line in lines:
            rep_file.write(line.line)

    def _export_REP(self, study, repertory, mage_rep, files, qlog, name="0"):

        if qlog is not None:
            qlog.put("Export REP file")

        # Write header
        with adists_file_open(
                os.path.join(
                    repertory, f"{name}.REP"
                ), "w+"
        ) as f:

            f.write(f"NET ../{mage_rep}/{name}.NET\n")
            f.write(f"REP ../{mage_rep}/{name}.REP\n")

            for file in files:
                EXT = file.split('.')[1]
                f.write(f"{EXT} {file}\n")

            self._export_REP_additional_lines(study, f)

        path_mage_net = os.path.join(os.path.abspath(os.path.join(repertory, os.pardir)), f"{mage_rep}/net")
        path_adists_net = os.path.join(repertory, "net")

        if os.path.exists(path_mage_net):
            shutil.copytree(path_mage_net, path_adists_net, dirs_exist_ok=True)

    @timer
    def export(self, study, repertory, qlog=None):
        self._study = study
        name = study.name.replace(" ", "_")

        self.export_additional_files(study, repertory, qlog, name=name)

        return True

    ###########
    # RESULTS #
    ###########

    def read_bin(self, study, repertory, results, qlog=None, name="0"):
        return

    @timer
    def results(self, study, repertory, qlog=None, name="0"):
        results = Results(
            study=study,
            solver=self,
            repertory=repertory,
            name=name,
        )
        self.read_bin(study, repertory, results, qlog, name=name)

        return results

    def output_param(self):
        name = ""
        return f"{name}"

################################
# Adis-TS in low coupling mode #
################################


class AdisTSlc(AdisTS):
    _type = "adistslc"

    def __init__(self, name):
        super(AdisTSlc, self).__init__(name)

        self._type = "adistslc"

    @classmethod
    def default_parameters(cls):
        lst = super(AdisTSlc, cls).default_parameters()

        # Insert new parameters at specific position
        names = list(map(lambda t: t[0], lst))

        return lst

    ##########
    # Export #
    ##########

    def cmd_args(self, study):
        lst = super(AdisTSlc, self).cmd_args(study)

        return lst

    def _export_POLs(self, study, repertory, qlog=None, name="0"):

        files = []

        if qlog is not None:
            qlog.put("Export POLS files")

        pollutants = study.river.Pollutants.Pollutants_List

        for pollutant in pollutants:
            name = pollutant.name
            with adists_file_open(os.path.join(repertory, f"{name}.POL"), "w+") as f:
                files.append(f"{name}.POL")
                f.write(f"*Polluant A contaminé aux PCB\n")
                f.write(f"name = {name}\n")

                self._export_POL_Characteristics(study, pollutant._data, f, qlog)

                POL_ICs = next(filter(lambda ic: ic.pollutant == pollutant.id,\
                                      study.river.initial_conditions_adists.Initial_Conditions_List))

                if POL_ICs.concentration != None:
                    f.write(f"file_ini = {name}.INI\n")
                    self._export_ICs_AdisTS(study, repertory, POL_ICs, qlog, name)

                POL_BCs = list(filter(lambda bc: bc.pollutant == pollutant.id,\
                                      study.river.boundary_conditions_adists.BCs_AdisTS_List))

                if len(POL_BCs) != 0:
                    f.write(f"file_cl = {name}.CDT\n")
                    self._export_BCs_AdisTS(study, repertory, POL_BCs, qlog, name)

                POL_LAT_Cont = list(filter(lambda lc: lc.pollutant == pollutant.id,\
                                      study.river.lateral_contributions_adists.Lat_Cont_List))

                if len(POL_LAT_Cont) != 0:
                    f.write(f"file_ald = {name}.ALD\n")
                    f.write(f"*\n")
                    self._export_Lat_AdisTS(study, repertory, POL_LAT_Cont, qlog, name)

        return files

    def _export_Lat_AdisTS(self, study, repertory, POL_LC, qlog, POL_name):

        if qlog is not None:
            qlog.put("Export POL LCs files")

        with adists_file_open(os.path.join(repertory, f"{POL_name}.ALD"), "w+") as f:
            for LC in POL_LC:
                reach_name = next(filter(lambda edge: edge.id == LC.edge, study.river.edges())).name
                f.write(f"${reach_name} {LC.begin_kp} {LC.end_kp}\n")
                f.write(f"*temps   |débit massique (kg/s)\n")
                f.write(f"*---------++++++++++\n")

                for LC_data in LC._data:
                    f.write(f"{timestamp_to_old_pamhyr_date_adists(int(LC_data[0]))} {LC_data[1]}\n")
                f.write(f"*\n")

        return True

    def _export_BCs_AdisTS(self, study, repertory, POL_BC, qlog, POL_name):

        if qlog is not None:
            qlog.put("Export POL BCs files")

        with adists_file_open(os.path.join(repertory, f"{POL_name}.CDT"), "w+") as f:
            for BC in POL_BC:
                node_name = next(filter(lambda x: x.id == BC.node, study.river._nodes)).name
                f.write(f"${node_name}\n")

                if BC.type == "Concentration":
                    f.write(f"*temps |concentration\n")
                    f.write(f"*JJ:HH:MM | (g/L)\n")
                    f.write(f"*---------++++++++++\n")
                else:
                    f.write(f"*temps |rate\n")
                    f.write(f"*JJ:HH:MM | (kg/s)\n")
                    f.write(f"*---------++++++++++\n")

                for BC_data in BC._data:
                    f.write(f"{timestamp_to_old_pamhyr_date_adists(int(BC_data[0]))} {BC_data[1]}\n")
                f.write(f"*\n")

        return True

    def _export_ICs_AdisTS(self, study, repertory, POL_IC_default, qlog, POL_name):

        if qlog is not None:
            qlog.put("Export POL ICs files")

        with adists_file_open(os.path.join(repertory, f"{POL_name}.INI"), "w+") as f:
            f.write(f"*État initial pour le polluant {POL_name}\n")
            f.write(f"{POL_IC_default.name} = {POL_IC_default.concentration} {POL_IC_default.eg} "+
            f"{POL_IC_default.em} {POL_IC_default.ed}\n")

            if len(POL_IC_default._data) != 0:
                self._export_ICs_AdisTS_Spec(study, POL_IC_default._data, f, qlog)

    def _export_ICs_AdisTS_Spec(self, study, pol_ics_spec_data, f, qlog, name="0"):

        for ic_spec in pol_ics_spec_data:
            f.write(f"{ic_spec.name} = {ic_spec.reach} {ic_spec.start_kp} {ic_spec.end_kp} " +
                    f"{ic_spec.concentration} {ic_spec.eg} {ic_spec.em} {ic_spec.ed} {ic_spec.rate}")

        return True

    def _export_POL_Characteristics(self, study, pol_data, f, qlog, name="0"):

        list_characteristics = ["type", "diametre", "rho", "porosity", "cdc_riv", "cdc_cas", "apd", "ac", "bc"]

        if len(list_characteristics) == (len(pol_data[0])-1):
            for l in range(len(list_characteristics)):
                f.write(f"{list_characteristics[l]} = {pol_data[0][l]}\n")

    def _export_D90(self, study, repertory, qlog=None, name="0"):

        files = []

        if qlog is not None:
            qlog.put("Export D90 file")

        with adists_file_open(os.path.join(repertory, f"{name}.D90"), "w+") as f:
            files.append(f"{name}.D90")

            f.write(f"*Diamètres caractéristiques du fond stable\n")

            d90AdisTS = study.river.d90_adists.D90_AdisTS_List

            f.write(f"{d90AdisTS[0].name} = {d90AdisTS[0].d90}\n")

            self._export_d90_spec(study, d90AdisTS[0]._data, f, qlog)

        return files

    def _export_d90_spec(self, study, d90_spec_data, f, qlog, name="0"):

        for d90_spec in d90_spec_data:
            if (d90_spec.name is None) or (d90_spec.reach is None) or (d90_spec.start_kp is None) or \
                (d90_spec.end_kp is None) or (d90_spec.d90 is None):
                return

            edges = study.river.enable_edges()

            id_edges = list(map(lambda x: x.id, edges))

            id_reach = d90_spec.reach

            if id_reach not in id_edges:
                return

            f.write(f"{d90_spec.name} = {id_reach} {d90_spec.start_kp} {d90_spec.end_kp} {d90_spec.d90}\n")

    def _export_DIF(self, study, repertory, qlog=None, name="0"):

        files = []

        if qlog is not None:
            qlog.put("Export DIF file")

        with adists_file_open(os.path.join(repertory, f"{name}.DIF"), "w+") as f:
            files.append(f"{name}.DIF")

            f.write(f"*Définition des paramètres des fonctions de calcul du\n")
            f.write(f"*coefficient de diffusion\n")

            difAdisTS = study.river.dif_adists.DIF_AdisTS_List

            if difAdisTS[0].method != "generique":
                f.write(f"defaut = {difAdisTS[0].method} {difAdisTS[0].dif }\n")
            else:
                f.write(f"defaut = {difAdisTS[0].method} {difAdisTS[0].dif} {difAdisTS[0].b} {difAdisTS[0].c}\n")

            self._export_dif_spec(study, difAdisTS[0]._data, f, qlog)

        return files

    def _export_dif_spec(self, study, dif_spec_data, f, qlog, name="0"):

        for dif_spec in dif_spec_data:
            if (dif_spec.reach is None) or (dif_spec.start_kp is None) or \
                (dif_spec.end_kp is None) or (dif_spec.dif is None) or (dif_spec.b is None) or (dif_spec.c is None):
                return

            edges = study.river.enable_edges()

            id_edges = list(map(lambda x: x.id, edges))

            id_reach = dif_spec.reach

            if id_reach not in id_edges:
                return

            if dif_spec.method != "generique":
                f.write(f"{dif_spec.method} = {id_reach} {dif_spec.start_kp} {dif_spec.end_kp} {dif_spec.dif}\n")
            else:
                f.write(f"{dif_spec.method} = {id_reach} {dif_spec.start_kp} {dif_spec.end_kp} {dif_spec.dif}" +
                f"{dif_spec.b} {dif_spec.c}\n")

    def _export_NUM(self, study, repertory, qlog=None, name="0"):

        dict_names = {"init_time":"start_date",
                      "final_time":"end_date",
                      "timestep":"dt0",
                      "implicitation_parameter":"theta",
                      "timestep_screen":"dtscr",
                      "timestep_bin":"dtbin",
                      "timestep_csv":"dtcsv",
                      "timestep_mage":"dtMage",
                      "initial_concentration":"c_initiale"}
        files = []

        if qlog is not None:
            qlog.put("Export NUM file")

        with adists_file_open(os.path.join(repertory, f"{name}.NUM"), "w+") as f:
            files.append(f"{name}.NUM")

            params = study.river.get_params(self.type).parameters
            for p in params:
                name = p.name\
                        .replace("all_", "")\
                        .replace("adists_", "")
                value = p.value

                logger.debug(
                    f"export: NUM: {name}: {value} ({p.value})"
                )

                if name != "command_line_arguments":
                    f.write(f"{dict_names[name]} = {value}\n")

            outputkps = study.river.Output_kp_adists.OutputKp_List

            for outputkp in outputkps:
                self._export_outputkp(study, outputkp, f, qlog)

        return files

    def _export_outputkp(self, study, outputkp, f, qlog, name="0"):
        if (outputkp.reach is None) or (outputkp.kp is None) or (outputkp.title is None):
            return

        edges = study.river.enable_edges()

        id_edges = list(map(lambda x: x.id, edges))

        id_reach = outputkp.reach
        kp = outputkp.kp
        title = outputkp.title

        if id_reach not in id_edges:
            return

        f.write(f"output = {id_reach} {kp} {title}\n")

    @timer
    def read_bin(self, study, repertory, results, qlog=None, name="0"):
        repertory_results = os.path.join(repertory, "resultats")

        files_bin_names = [el.split("/")[-1] for el in glob.glob(repertory_results+"/*.bin")]
        print("files names resultats: ", files_bin_names)

        ifilename = os.path.join(repertory_results, files_bin_names[0])

        logger.info(f"read_bin: Start reading '{ifilename}' ...")

        print("reading ", ifilename)
        with open(ifilename, 'rb') as f:
            # header
            # first line
            data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (start)
            data = np.fromfile(f, dtype=np.int32, count=3)
            ibmax = data[0]  # number of reaches
            ismax = data[1]  # total number of cross sections
            kbl = data[2] * -1  # block size for .BIN header
            data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (end)
            # second line
            data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (start)
            ibu = np.fromfile(f, dtype=np.int32, count=ibmax)
            data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (end)
            # third line
            data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (start)
            data = np.fromfile(f, dtype=np.int32, count=2 * ibmax)
            is1 = np.zeros(ibmax, dtype=np.int32)
            is2 = np.zeros(ibmax, dtype=np.int32)
            print("nombre de biefs : ", ibmax)

            logger.debug(f"read_bin: nb_reach = {ibmax}")
            logger.debug(f"read_bin: nb_profile = {ismax}")

            results.set("nb_reach", f"{ibmax}")
            results.set("nb_profile", f"{ismax}")

            reachs = []
            iprofiles = {}
            reach_offset = {}

            for i in range(ibmax):
                # Add results reach to reach list
                r = results.river.add(i)
                reachs.append(r)

                is1[i] = data[2 * i]  # first section of reach i (FORTRAN numbering)
                is2[i] = data[2 * i + 1]  # last section of reach i (FORTRAN numbering)

                key = (is1[i], is2[i])
                iprofiles[key] = r

                reach_offset[r] = is1[i]

            logger.debug(f"read_bin: iprofiles = {iprofiles}")

            data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (end)
            # fourth line
            pk = np.zeros(ismax, dtype=np.float32)
            for k in range(0, ismax, kbl):
                data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (start)
                pk[k:min(k + kbl, ismax)] = np.fromfile(f, dtype=np.float32, count=min(k + kbl, ismax) - k)
                print("pk : ", pk)
                data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (end)

                # fifth line (useless)
                data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (start)
                zmin_OLD = np.fromfile(f, dtype=np.float32, count=1)[0]
                print("zmin_OLD : ", zmin_OLD)
                data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (end)
                # sixth line
                zf = np.zeros(ismax, dtype=np.float32)
                z = np.zeros(ismax * 3, dtype=np.float32)
                for k in range(0, ismax, kbl):
                    data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (start)
                    z[3 * k:3 * min(k + kbl, ismax)] = np.fromfile(f, dtype=np.float32,
                                                                   count=3 * (min(k + kbl, ismax) - k))
                    # z[i*3+1] and z[i*3+2] are useless
                    data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (end)
                zf = [z[i * 3] for i in range(ismax)]
                print("zf : ", zf)
                # seventh line (useless)
                for k in range(0, ismax, kbl):
                    data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (start)
                    zero = np.fromfile(f, dtype=np.int32, count=ismax)
                    print("zero : ", zero)
                    data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (end)
                # end header

        def ip_to_r(i): return iprofiles[
            next(
                filter(
                    lambda k: k[0] <= i <= k[1],
                    iprofiles
                )
            )
        ]

        def ip_to_ri(r, i): return i - reach_offset[r]

        path_files = map(lambda file: os.path.join(repertory_results, file), files_bin_names)

        data_tmp = {}

        for file_bin in path_files:
            key_pol = file_bin.split("/")[-1][0:-4]
            data_tmp[key_pol] = {}
            with open(file_bin, 'rb') as f:
                # header
                # first line
                data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (start)
                data = np.fromfile(f, dtype=np.int32, count=3)
                ibmax = data[0]  # number of reaches
                ismax = data[1]  # total number of cross sections
                kbl = data[2] * -1  # block size for .BIN header
                data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (end)
                # second line
                data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (start)
                ibu = np.fromfile(f, dtype=np.int32, count=ibmax)
                data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (end)
                # third line
                data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (start)
                data = np.fromfile(f, dtype=np.int32, count=2 * ibmax)
                is1 = np.zeros(ibmax, dtype=np.int32)
                is2 = np.zeros(ibmax, dtype=np.int32)
                for i in range(ibmax):
                    is1[i] = data[2 * i]  # first section of reach i (FORTRAN numbering)
                    is2[i] = data[2 * i + 1]  # last section of reach i (FORTRAN numbering)
                data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (end)
                # fourth line
                pk = np.zeros(ismax, dtype=np.float32)
                for k in range(0, ismax, kbl):
                    data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (start)
                    pk[k:min(k + kbl, ismax)] = np.fromfile(f, dtype=np.float32, count=min(k + kbl, ismax) - k)
                    data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (end)
                # fifth line (useless)
                data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (start)
                zmin_OLD = np.fromfile(f, dtype=np.float32, count=1)[0]
                data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (end)
                # sixth line
                zf = np.zeros(ismax, dtype=np.float32)
                z = np.zeros(ismax * 3, dtype=np.float32)
                for k in range(0, ismax, kbl):
                    data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (start)
                    z[3 * k:3 * min(k + kbl, ismax)] = np.fromfile(f, dtype=np.float32,
                                                                   count=3 * (min(k + kbl, ismax) - k))
                    # z[i*3+1] and z[i*3+2] are useless
                    data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (end)
                zf = [z[i * 3] for i in range(ismax)]
                # seventh line (useless)
                for k in range(0, ismax, kbl):
                    data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (start)
                    zero = np.fromfile(f, dtype=np.int32, count=ismax)
                    data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (end)
                # end header
                # data
                data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (start)
                while data.size > 0:
                    ismax = np.fromfile(f, dtype=np.int32, count=1)[0]
                    t = np.fromfile(f, dtype=np.float64, count=1)[0]
                    if not t in data_tmp[key_pol]:
                        data_tmp[key_pol][t] = {}
                    c = np.fromfile(f, dtype=np.byte, count=1)
                    # possible values :
                    # sediment : C, G, M, D, L, N, R
                    # polutant : C, G, M, D
                    phys_var = bytearray(c).decode()
                    data_tmp[key_pol][t][phys_var] = {}
                    real_data = np.fromfile(f, dtype=np.float32, count=ismax)
                    data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (end)
                    data_tmp[key_pol][t][phys_var] = real_data
                    data = np.fromfile(f, dtype=np.int32, count=1)  # line length (bytes) (start)
                # end data

        print(data_tmp["AAA-silt"])

        pollutants_keys = list(data_tmp.keys())
        timestamps_keys = list(data_tmp[pollutants_keys[0]].keys())
        phys_data_names = list(data_tmp[pollutants_keys[0]][timestamps_keys[0]].keys())

        print("pol keys: ", pollutants_keys)
        print("t keys: ", timestamps_keys)
        print("phys var: ", phys_data_names)

        for i in range(ismax):
            reach = ip_to_r(i)
            p_i = ip_to_ri(reach, i)

            for t_data in timestamps_keys:
                pol_view = []
                for pol in pollutants_keys:
                    pol_view.append(set(data_tmp[pol][t_data].values()))

                reach.set(p_i, t_data, "pols", pol_view)

    @timer
    def results(self, study, repertory, qlog=None, name=None):
        self._study = study
        if name is None:
            name = study.name.replace(" ", "_")

        results = super(AdisTSlc, self).results(study, repertory, qlog, name=name)

        return results

    def export_func_dict(self):
        return [
            self._export_NUM,
            self._export_DIF,
            self._export_D90,
            self._export_POLs,
        ]

    @timer
    def export(self, study, repertory, mage_rep, qlog=None, name="0"):
        print("cmd solver adistslc : ", self._cmd_solver)
        self._study = study
        name = study.name.replace(" ", "_")

        # Generate files
        files = []

        try:
            for func in self.export_func_dict():
                files = files + func(study, repertory, qlog, name=name)

            self.export_additional_files(study, repertory, qlog, name=name)
            self._export_REP(study, repertory, mage_rep, files, qlog, name=name)

            return True
        except Exception as e:
            logger.error(f"Failed to export study to {self._type}")
            logger_exception(e)
            return False