nmreval/src/gui_qt/main/management.py

from __future__ import annotations

import pathlib
import re
import uuid

import numpy as np

from nmreval.fit import data as fit_d
from nmreval.fit.model import Model
from nmreval.fit.result import FitResult
from nmreval.fit.minimizer import FitRoutine
from nmreval.lib.colors import available_cycles
from nmreval.lib.logger import logger
from nmreval.math.interpol import interpolate
from nmreval.math.logfourier import logft
from nmreval.math.smooth import smooth
from nmreval.nmr.relaxation import Relaxation

from ..Qt import QtCore, QtWidgets
from ..lib.undos import *
from ..data.container import *
from ..io.filereaders import QFileReader
from ..lib.utils import busy_cursor


class GraphSignals(QtCore.QObject):
    valueChanged = QtCore.pyqtSignal()


class GraphDict(OrderedDict):
    def __init__(self, data):
        super().__init__()

        self._data = data
        self.signals = GraphSignals()
        self.valueChanged = self.signals.valueChanged

    def __setitem__(self, key, value):
        super().__setitem__(key, value)
        self.valueChanged.emit()

    def __delitem__(self, key):
        super().__delitem__(key)
        self.valueChanged.emit()

    def tree(self, key_only=False):
        ret_val = OrderedDict()
        for k, g in self.items():
            if key_only:
                ret_val[k] = (g.title, [(s, self._data[s].name) for s in g.sets])
            else:
                ret_val[(k, g.title)] = [(s, self._data[s].name) for s in g.sets]

        return ret_val

    def list(self):
        return [(k, v.title) for k, v in self.items()]

    def active(self, key: str):
        if key:
            return [(self._data[i].id, self._data[i].name) for i in self[key]]
        else:
            return []

    def current_sets(self, key: str):
        if key:
            return [(self._data[i].id, self._data[i].name) for i in self[key].sets]
        else:
            return []


class UpperManagement(QtCore.QObject):
    newGraph = QtCore.pyqtSignal()
    restoreGraph = QtCore.pyqtSignal(str)
    deleteGraph = QtCore.pyqtSignal(str)
    newData = QtCore.pyqtSignal([list, str], [list, str, bool])
    deleteData = QtCore.pyqtSignal(list)
    dataChanged = QtCore.pyqtSignal(str)
    fitFinished = QtCore.pyqtSignal(list)
    stopFit = QtCore.pyqtSignal()
    properties_collected = QtCore.pyqtSignal(dict)
    unset_state = QtCore.pyqtSignal(list)

    _colors = cycle(TUColors)

    _actions = {
        'ls': (ShiftCommand, 'Left shift'),
        'cut': (CutCommand, 'Cut'),
        'ap': (ApodizationCommand, 'Apodization'),
        'zf': (ZerofillCommand, 'Zerofill'),
        'ph': (PhaseCommand, 'Phase correction'),
        'autoph': (AutophaseCommand, 'Autophase'),
        'bl': (BaselineCommand, 'Baseline'),
        'bls': (BaselineSplineCommand, 'Baseline'),
        'ft': (FourierCommand, 'Fourier'),
        'ft_pake': 'FT (de-paked)',
        'sort': (SortCommand, 'Sort'),
        'norm': (NormCommand, 'Normalize'),
        'center': (CenterCommand, 'Center on max'),
    }

    def __init__(self, window):
        super().__init__()

        self._fit_active = False
        self.fit_thread = None
        self.fit_worker = None

        self.counter = 0
        self.data = OrderedDict()
        self.window = window
        self.current_graph = None
        self.graphs = GraphDict(self.data)
        self.namespace = None
        self.undostack = QtWidgets.QUndoStack()
        self.deleteData.connect(self.plot_from_graph)

        self._filereader = None

    def __setitem__(self, key: str, value, **kwargs):
        if isinstance(value, ExperimentContainer):
            item = value
            item.id = key
        elif isinstance(value, FitResult):
            item = FitContainer(key, value, manager=self, **kwargs)
        elif isinstance(value, Signal):
            item = SignalContainer(key, value, manager=self, **kwargs)
        else:
            item = PointContainer(key, value, manager=self, **kwargs)

        item.dataChanged.connect(lambda x: self.dataChanged.emit(x))

        self.data[key] = item

    def __getitem__(self, item):
        return self.data[item]

    def __contains__(self, item):
        return item in self.data

    def __iter__(self):
        for k, v in self.data.items():
            yield k, v

    @property
    def active_sets(self):
        return self.graphs.active(self.current_graph)

    def get_attributes(self, graph_id: str, attr: str) -> dict[str, Any]:
        return {self.data[i].id: getattr(self.data[i], attr) for i in self.graphs[graph_id].sets}

    def add(self, data, **kwargs):
        _id = str(uuid.uuid4())
        self.__setitem__(_id, data, **kwargs)

        return _id

    def load_files(self, fname: list[str], new_plot: str = None):
        if self._filereader is None:
            self._filereader = QFileReader(manager=self)
        ret_dic = self._filereader.readfiles(fname)
        self.add_new_data(ret_dic, new_plot)

    def _load_session(self, sets: dict, graphs: dict):
        sid = self._load_sets(sets)

        for g in graphs:
            _ = g.pop('id')
            graph = QGraphWindow.set_state(g)
            self.graphs[graph.id] = graph
            self.restoreGraph.emit(graph.id)

            children = [sid[c] for c in g['children']]
            active = [sid[c] for c in g['active']]
            inactive = [k for k in children if k not in active]

            self.newData.emit(children, graph.id)

            graph.active = active
            graph.listWidget.blockSignals(True)
            for i, l in enumerate(g['in_legend']):
                try:
                    graph.listWidget.item(i).setCheckState(QtCore.Qt.Checked if l else QtCore.Qt.Unchecked)
                except AttributeError:
                    pass
            graph.listWidget.blockSignals(False)

            #  set unchecked in tree and hide/show in plot
            self.unset_state.emit(inactive)
            self.change_visibility(active, inactive)

    def _load_sets(self, sets: dict) -> dict:
        sid = {}
        for _id, (data, opts) in sets.items():
            if isinstance(data, FitResult):
                # for fits, _id belongs to the fitted data, not the fit
                src_id = data.idx
                if src_id in sid:
                    new_id = self.add(data, src=sid[src_id])
                    self.data[sid[src_id]]._fits.append(new_id)
                else:
                    new_id = self.add(data)
            else:
                new_id = self.add(data)

            sid[_id] = new_id

            for m in ['real', 'imag']:
                if m in opts:
                    self.data[new_id].setSymbol(**opts[m][0], mode=m)
                    self.data[new_id].setLine(**opts[m][1], mode=m)

        return sid

    def add_new_data(self, data: list, gid: str):
        sid = []
        for d in data:
            if isinstance(d, tuple):
                if len(d) == 2:
                    self._load_session(d[0], graphs=d[1])
                else:
                    sid.extend(list(self._load_sets(d[0]).values()))
            else:
                sid.append(self.add(d))

        if sid:
            gid = '' if not gid else gid

            self.newData.emit(sid, gid)

    def plots_to_graph(self, plotkeys: list, gid: str):
        self.graphs[gid].add(plotkeys, [self.data[k].plots for k in plotkeys])
        for k in plotkeys:
            self.data[k].graph = gid

    @QtCore.pyqtSlot(list)
    def plot_from_graph(self, key: list[str]):
        sort_graph = {}
        for sid in key:
            v = self.data[sid].graph
            if v not in sort_graph:
                sort_graph[v] = []
            sort_graph[v].append(sid)

        for gid, sets in sort_graph.items():
            self.graphs[gid].remove(sets)

    @QtCore.pyqtSlot(list, str, str)
    def move_sets(self, sets: list, dest: str, src: (str|list), pos: int = -1):
        if isinstance(src, str):
            src = [src]*len(sets)

        for graph_id, set_id in zip(src, sets):
            # move all plots to the same graph
            if graph_id != dest:
                self.graphs[graph_id].remove(set_id)
                self.plots_to_graph([set_id], dest)

        # move to correct position
        self.graphs[dest].move_sets(sets, pos)

    def select_window(self, gid: str):
        for key, plot in self.graphs.items():
            if key == gid:
                self.window.area.setActiveSubWindow(plot.parent())

    @QtCore.pyqtSlot()
    @QtCore.pyqtSlot(list, str)
    def copy_sets(self, sets: list = None, src: str = None):
        if sets is None:
            sets = self.graphs[self.current_graph].active[:]

        if src is None:
            src = self.current_graph

        new_ids = []
        for s in sets:
            copy_of_s = self.data[s].copy(full=True)
            copy_of_s.id = str(uuid.uuid4())
            new_ids.append(copy_of_s.id)
            self.data[copy_of_s.id] = copy_of_s

        self.newData.emit(new_ids, src)

        return new_ids

    @QtCore.pyqtSlot(list)
    @QtCore.pyqtSlot(str)
    @QtCore.pyqtSlot()
    def delete_sets(self, rm_sets: list = None):
        rm_graphs = []

        if rm_sets is None:
            rm_sets = self.graphs[self.current_graph].sets + [self.current_graph]

        self.undostack.beginMacro('Delete')

        rm_set_by_graph = {}

        for k in rm_sets[::-1]:
            if k in self.data:
                parent_graph = self.data[k].graph
                if parent_graph not in rm_set_by_graph:
                    rm_set_by_graph[parent_graph] = []

                rm_set_by_graph[parent_graph].append(k)

            elif k in self.graphs:
                rm_graphs.append(k)

            else:
                logger.warning(f'delete_sets: {k} is not in data or graph found')

        for gid, sid_list in rm_set_by_graph.items():
            cmd = DeleteCommand(self.data, sid_list, self.graphs, gid, self.newData, self.deleteData)
            self.undostack.push(cmd)

        for k in rm_graphs:
            cmd = DeleteGraphCommand(self.graphs, k, self.restoreGraph, self.deleteGraph)
            self.undostack.push(cmd)

        self.undostack.endMacro()

    def delete_graph(self, gid):
        self.delete_sets(self.graphs[gid].sets + [gid])

    @QtCore.pyqtSlot()
    def cat(self, src_sets=None):
        joined = None
        group_set = set()
        name_set = set()
        value_set = set()

        if src_sets is None:
            if self.current_graph:
                src_sets = self.graphs[self.current_graph].active
            else:
                return

        for sid in src_sets:
            data_i = self.data[sid]
            if joined is None:
                joined = data_i.copy()
            else:
                joined.append(data_i.x, data_i.y, data_i.y_err)

            name_set.add(data_i.name)
            group_set.add(data_i.group)
            value_set.add(data_i.value)

        if joined is not None:
            joined.group = '+'.join(group_set)
            joined.name = '+'.join(name_set)

            if len(value_set) == 1:
                joined.value = value_set.pop()
            else:
                joined.value = 0.0

            self.newData.emit([self.add(joined)], self.current_graph)

    def get_data(self, sid: str, xy_only: bool = False):
        """
        Return data for a given id.
        Return value is tuple of [x, y, y_err] and mask if xy_only is False, [x, y] if true.
        """
        d = self.data[sid]
        if xy_only:
            return [d.x, d.y]

        return [d.data.x, d.data.y, d.data.y_err], d.data.mask.data

    def change_visibility(self, selected: list, deselected: list):
        """Change status of list of ids after status change in datawidget"""

        for s in selected:
            self.graphs[self.data[s].graph].show_item([s])

        for d in deselected:
            self.graphs[self.data[d].graph].hide_item([d])

    @QtCore.pyqtSlot(str, str)
    def change_keys(self, identifier: str, name: str):
        if identifier in self.data:
            d = self.data[identifier]
            d.name = name
            self.graphs[d.graph].update_legend(identifier, name)
        elif identifier in self.graphs:
            self.graphs[identifier].title = name
        else:
            raise KeyError('Unknown ID ' + str(identifier))

    @QtCore.pyqtSlot(str, tuple)
    def apply(self, func: str, arguments: tuple):
        # undos, names displayed by undo action
        cmd, cmd_text = self._actions[func]

        self.undostack.beginMacro(cmd_text)
        for sid in self.graphs[self.current_graph]:
            single_undo = cmd(self.data[sid], *arguments)
            self.undostack.push(single_undo)
        self.undostack.endMacro()

    def cut(self):
        if self.current_graph:
            xlim, _ = self.graphs[self.current_graph].ranges
            self.apply('cut', xlim)

    @QtCore.pyqtSlot()
    def unmask(self):
        for d in self.data.values():
            d.mask = np.ones_like(d.mask, dtype=bool)

    def start_fit(self, parameter: dict, links: list, fit_options: dict):
        if self._fit_active:
            return

        self.__fit_options = (parameter, links, fit_options)

        self.fitter = FitRoutine()
        models = {}
        fit_limits = fit_options['limits']
        fit_mode = fit_options['fit_mode']
        we = fit_options['we']

        for model_id, model_p in parameter.items():
            m = Model(model_p['func'])
            models[model_id] = m

            m_complex = model_p['complex']

            for set_id, set_params in model_p['parameter'].items():
                data_i = self.data[set_id]
                if we.lower() == 'deltay':
                    we = data_i.y_err**2

                if m_complex is None or m_complex == 1:
                    _y = data_i.y.real
                elif m_complex == 2 and np.iscomplexobj(data_i.y):
                    _y = data_i.y.imag
                else:
                    _y = data_i.y

                _x = data_i.x

                if fit_limits == 'none':
                    inside = slice(None)
                elif fit_limits == 'x':
                    x_lim, _ = self.graphs[self.current_graph].ranges
                    inside = np.where((_x >= x_lim[0]) & (_x <= x_lim[1]))
                else:
                    inside = np.where((_x >= fit_limits[0]) & (_x <= fit_limits[1]))

                if isinstance(we, str):
                    d = fit_d.Data(_x[inside], _y[inside], we=we, idx=set_id)
                else:
                    d = fit_d.Data(_x[inside], _y[inside], we=we[inside], idx=set_id)

                d.set_model(m)
                d.set_parameter(set_params[0], var=model_p['var'],
                                lb=model_p['lb'], ub=model_p['ub'],
                                fun_kwargs=set_params[1])

                self.fitter.add_data(d)

            model_globs = model_p['glob']
            if model_globs:
                m.set_global_parameter(**model_p['glob'])

        for links_i in links:
            self.fitter.set_link_parameter((models[links_i[0]], links_i[1]),
                                           (models[links_i[2]], links_i[3]))

        with busy_cursor():
            self.fit_worker = FitWorker(self.fitter, fit_mode)
            self.fit_thread = QtCore.QThread()
            self.fit_worker.moveToThread(self.fit_thread)

            self.fit_thread.started.connect(self.fit_worker.run)
            self.fit_worker.finished.connect(self.end_fit)
            self.fit_worker.finished.connect(self.fit_thread.quit)
            self.fit_worker.finished.connect(self.fit_worker.deleteLater)
            self.fit_thread.finished.connect(self.fit_thread.deleteLater)

            self.stopFit.connect(lambda: self.fit_worker.fitter.abort())

            self.fit_thread.start()

    @QtCore.pyqtSlot(list, bool)
    def end_fit(self, result: list, success: bool):
        if success:
            logger.info('Successful fit')
            self.fitFinished.emit(result)
        else:
            e = result[0]
            logger.exception(e, exc_info=True)
            QtWidgets.QMessageBox.warning(QtWidgets.QWidget(), 'Fit failed',
                                          f'Fit kaput with exception: \n\n{e!r}')
            self.fitFinished.emit([])
        self._fit_active = False

    @QtCore.pyqtSlot(dict)
    def redo_fits(self, res: dict):
        models = self.__fit_options[0]
        for single_model, model_args in models.items():
            parameter = model_args['parameter']

            for set_id, set_parameter in parameter.items():
                new_values = [v.value for v in res[set_id].parameter.values()]
                parameter[set_id] = (new_values, set_parameter[1])
        self.start_fit(*self.__fit_options)

    def make_fits(self, res: dict, opts: list, param_graph: str, show_fit: bool, parts: bool, extrapolate: list) -> None:
        """

        Args:
            res: key is that of original data, value is FitResult
            opts: (ignore this fits, delete previous fits)
            param_graph: None if no parameter to plot, '' for new graph, or id of existig graph
            show_fit: plot fit curve?
            parts: key is that of original data, value is list of subplots
            extrapolate:

        """
        f_id_list = []
        gid = ''

        tobedeleted = []
        accepted = []
        for i, (k, fit) in enumerate(res.items()):
            reject, delete_prev = opts[i]
            if reject:
                continue

            if not all(e is None for e in extrapolate):
                spacefunc = np.geomspace if fit.islog else np.linspace

                xmin = fit.x.min()
                xmax = fit.x.max()

                len_data = len(fit.x_data)
                num_pts = 20*len_data-9 if len_data < 51 else 3*len_data

                if extrapolate[0] is not None:
                    xmin = extrapolate[0]
                if extrapolate[1] is not None:
                    xmax = extrapolate[1]
                if extrapolate[2] is not None:
                    num_pts = extrapolate[2]

                _x = spacefunc(xmin, xmax, num=num_pts)

                fit = fit.with_new_x(_x)

            data_k = self.data[k]
            if delete_prev:
                tobedeleted.extend([f.id for f in data_k.get_fits()])
                data_k.set_fits([])

            syms = data_k.plot_real.symbol
            if syms == SymbolStyle.No:
                color = data_k.plot_real.linecolor
            else:
                color = data_k.plot_real.symbolcolor

            fit.value = data_k.value
            fit.group = data_k.group

            accepted.append(fit)

            data_name = f' ({data_k.name})'
            if show_fit:
                fit.name += data_name
                f_id = self.add(fit, color=color, src=k)

                f_id_list.append(f_id)
                data_k.set_fits(f_id)

                if parts:
                    color_scheme = available_cycles['colorblind']
                    for subfunc, col in zip(fit.sub(fit.x), cycle(color_scheme)):
                        subfunc.value = data_k.value
                        subfunc.group = data_k.group
                        subfunc.name += data_name
                        sub_f_id = self.add(subfunc, color=col, linestyle=LineStyle.Dashed, symbol=SymbolStyle.No)

                        f_id_list.append(sub_f_id)
            gid = data_k.graph
        self.delete_sets(tobedeleted)

        if accepted and (param_graph != '-1'):
            self.make_fit_parameter(accepted, graph_id=param_graph)

        self.newData.emit(f_id_list, gid)

    def extend_fits(self, set_id: list, x_range: np.ndarray):
        graphs = {}
        for sid in set_id:
            data = self[sid]
            fit = data.copy(full=True, keep_color=True)
            fit.data = fit.data.with_new_x(x_range)

            graph_id = data.graph
            if graph_id not in graphs:
                graphs[graph_id] = []
            graphs[graph_id].append(self.add(fit))

            color_scheme = available_cycles['colorblind']
            for subfunc, col in zip(fit.data.sub(fit.x), cycle(color_scheme)):
                subfunc.value = fit.value
                subfunc.group = fit.group
                graphs[graph_id].append(self.add(subfunc, color=col, linestyle=LineStyle.Dashed, symbol=SymbolStyle.No))

        for k, v in graphs.items():
            self.newData.emit(v, k)

    def make_fit_parameter(self, fit_sets: list[str | FitResult], graph_id: str = None):
        fit_dict = self._collect_fit_parameter(fit_sets)

        if fit_dict:
            p_id_list = []
            for v in fit_dict.values():
                xy = np.array(v[0]).T
                p_id_list.append(self.add(Points(x=xy[0], y=xy[1], y_err=xy[2], name=v[1])))

            if not graph_id:
                graph_id = ''

            self.newData[list, str, bool].emit(p_id_list, graph_id, True)

    def save_fit_parameter(self, fname: str | pathlib.Path, fit_sets: list[str] = None):
        if fit_sets is None:
            fit_sets = [s for (s, _) in self.active_sets]

        for set_id in fit_sets:
            data = self.data[set_id]
            if data.mode != 'fit':
                continue

            data.data.save_parameter(fname)

    def _collect_fit_parameter(self, fit_sets: list[str | FitResult]) -> dict:
        fit_dict = {}

        for set_id in fit_sets:
            if isinstance(set_id, str):
                data = self.data[set_id]
                if data.mode != 'fit':
                    continue
            elif isinstance(set_id, FitResult):
                data = set_id
            else:
                continue

            for key, pvalue in data.parameter.items():
                name = pvalue.full_name
                fit_key = key + data.model_name

                if fit_key not in fit_dict:
                    fit_dict[fit_key] = [[], name]

                err = 0 if pvalue.error is None else pvalue.error

                fit_dict[fit_key][0].append([data.value, pvalue.value, err])

        return fit_dict

    @QtCore.pyqtSlot(dict, str)
    def extract_points(self, params: dict, gid: str):
        xy_mode = params.pop('xy')
        _active = self.graphs[self.current_graph].active

        new_datasets = {}
        for sid in _active:
            data_i = self.data[sid]
            if data_i.group not in new_datasets:
                new_datasets[data_i.group] = [], []
            new_x_axis, _temp = new_datasets[data_i.group]

            new_x_axis.append(data_i.value)
            _temp.append(data_i.points(params))

        key_list = []
        for label, (new_x_axis, _temp) in new_datasets.items():
            _temp = np.array(_temp)  # (number of sets, number of picks, (x, y, y_err))
            num_pts = _temp.shape[1]

            for i in range(num_pts):
                if xy_mode[0]:
                    key = self.add(Points(x=new_x_axis, y=_temp[:, i, 0], name=label))
                    key_list.append(key)

                if xy_mode[1]:
                    key = self.add(Points(x=new_x_axis, y=_temp[:, i, 1], y_err=_temp[:, i, 2], name=label))
                    key_list.append(key)

        self.newData.emit(key_list, gid)

    @QtCore.pyqtSlot(list)
    def get_properties(self, sid: list) -> dict:
        props = {}
        for key in sid:
            if key not in self.data:
                continue

            props = self.data[key].get_properties()

        self.properties_collected.emit(props)

        return props

    @QtCore.pyqtSlot(list, str, str, object)
    def update_property(self, sid: list, key1: str, key2: str, value: Any):
        for s in sid:
            self.data[s].update_property(key1, key2, value)

    def create_empty(self):
        import numpy.random as random
        dat = Points(x=np.arange(10), y=np.arange(10) + random.rand(10)-0.5, y_err=random.rand(10),
                     name='Das Sein und das Nichts')
        idd = self.add(dat)
        self.newData.emit([idd], self.current_graph)

    @QtCore.pyqtSlot(tuple, dict, str)
    def calc_mean(self, dist_params, conversion, graph):
        dist, args = dist_params
        parameter = []

        x = None
        name = 'tau (%s)' % {conversion["to_"]}
        value = 0.
        for i, p in enumerate(args):
            if isinstance(p, float):
                parameter.append(p)
            else:
                if x is None:
                    x = self.data[p].x
                    if i == 0:
                        name = self.data[p].name
                        value = self.data[p].value
                parameter.append(self.data[p].y)

        if x is None:
            x = 0

        key = self.add(Points(x, dist.convert(*parameter, **conversion), name=name, value=value))
        self.newData.emit([key], graph)
        self.sender().update_graphs(self.graphs.tree(key_only=True))

    @QtCore.pyqtSlot(list, str, bool, bool, tuple, str)
    def interpolate_data(self, data_ids, mode, xlog, ylog, new_axis, dest_graph):
        if len(new_axis) == 4:
            start, end, steps, loggy = new_axis
            if loggy:
                new_x = np.logspace(np.log10(start), np.log10(end), steps)
            else:
                new_x = np.linspace(start, end, steps)
        else:
            new_x = self.data[new_axis[0]].x

        new_key = []
        for ids in data_ids:
            k = self.add(interpolate(self.data[ids], new_x, xlog=xlog, ylog=ylog, kind=mode, extrapolate=True))
            new_key.append(k)

        self.newData.emit(new_key, dest_graph)

    def binning(self, digits: int):
        _active = self.graphs[self.current_graph].active
        new_data = []
        for sid in _active:
            key = self.add(self.data[sid].binning(digits=digits))
            new_data.append(key)

        self.newData.emit(new_data, self.current_graph)

    @QtCore.pyqtSlot(dict, dict, str)
    def addTg(self, dic1: dict, dic2: dict, graph_id: str):
        for k, v in dic1.items():
            p: ExperimentContainer = self[k]
            col = p.plot_real.linecolor
            set_id = self.add(v[0], color=col)
            self.newData.emit([set_id], self.current_graph)
            for line in v[1]:
                set_id = self.add(line, color=col)
                self.newData.emit([set_id], self.current_graph)

        set_id_list = []
        for v in dic2.values():
            set_id_list.append(self.add(v))
        self.newData.emit(set_id_list, '')

    @QtCore.pyqtSlot(int, dict)
    def smooth_data(self, npoints, param_kwargs):
        _active = self.graphs[self.current_graph].active
        new_data = []
        for sid in _active:
            try:
                key = self.add(smooth(self.data[sid], npoints, **param_kwargs))
                new_data.append(key)
            except Exception as e:
                QtWidgets.QMessageBox().warning(self.window,
                                                'Smoothing failed!',
                                                f'Smoothing failed for {self.data[sid].name} with exception:\n{e.args}')
        if new_data:
            self.newData.emit(new_data, self.current_graph)

    @QtCore.pyqtSlot()
    def set_cycle(self, set_idx: list, cycle_name: str):
        col = cycle(available_cycles[cycle_name])
        for s_id in set_idx:
            self.data[s_id].setColor(next(col), symbol=True, line=True, mode='all')

    @QtCore.pyqtSlot(dict, tuple)
    def shift_scale(self, values: dict, options: tuple):
        copy_data, value_plot = options

        sid_list = []
        shift_y = []
        shift_x = []
        for k, v in values.items():
            d_k = self.data[k]

            if copy_data is None:
                d_k.x = d_k.x*v[1][0] + v[0][0]
                d_k.y = d_k.y*v[1][1] + v[0][1]
            else:
                new_data = d_k.copy(full=True)
                new_data.update({'shift': v[0], 'scale': v[1]})
                new_data.data.x = new_data.x*v[1][0] + v[0][0]
                new_data.y = new_data.y*v[1][1] + v[0][1]

                sid = self.add(new_data)
                sid_list.append(sid)

            shift_x.append(d_k.value)
            shift_y.append(v[0]+v[1])

        self.newData.emit(sid_list, copy_data)

        if value_plot is not None:
            sid_list = []
            shift_y = np.array(shift_y)
            for i, (mode, default) in enumerate([('x shift', 0.), ('y shift', 0.),
                                                 ('x scale', 1.), ('y scale', 1.), ]):
                if np.all(shift_y[:, i] == default):
                    continue
                data = Points(shift_x, shift_y[:, i], name=mode)
                sid_list.append(self.add(data))

            self.newData.emit(sid_list, value_plot)

    @QtCore.pyqtSlot(list)
    def convert_sets(self, src: list):
        new_graph = {}

        error_list = []

        for sets in src:
            # merge: sets (real, imag, graph, type)
            # normal: sets (source set, graph, type)

            graph_id = sets[-2]
            new_type = [Points, FID, Spectrum, BDS][sets[-1]]

            if len(sets) == 4:
                real_set, imag_set = sets[0], sets[1]
                if real_set != '':
                    data = self.data[real_set]
                    new_data = new_type(data.x, data.y.real)
                    if imag_set != '':
                        imag_data = self.data[imag_set]
                        if len(imag_data) == len(data):
                            new_data.y.imag = imag_data.y.real
                        else:
                            error_list.append(f'Lengths mismatch of {data.name} ({len(data)}) and {imag_data.name} ({len(imag_data)})')
                            continue

                else:
                    data = self.data[imag_set]
                    new_data = new_type(data.x, np.zeros(data.x.size))
                    new_data.y.imag = data.y.real

            else:
                data = self.data[sets[0]]
                if isinstance(data.data, new_type):
                    error_list.append(f'{data.name} is alreade of type {new_type.__name__}')
                    continue

                new_data = new_type(data.x, np.zeros(data.x.size))
                new_data.y.real = data.y.real

            new_data.update(data.opts)
            new_id = self.add(data.change_type(new_data))
            if graph_id not in new_graph:
                new_graph[graph_id] = []

            new_graph[graph_id].append(new_id)

        for g, s in new_graph.items():
            self.newData.emit(s, g)

        if error_list:
            err_string = "\n- ".join(error_list)
            _ = QtWidgets.QMessageBox.information(QtWidgets.QWidget(), 'Something was skipped',
                                                  f'Some conversions were skipped:\n{err_string}')

    def get_namespace(self):
        from ..lib.namespace import Namespace
        self.namespace = Namespace(basic=True, const=True, fitfuncs=True)

        for i, g in enumerate(self.graphs.values()):
            for j, sid in enumerate(g.sets):
                sets = self.data[sid]
                self.namespace.add_namespace(sets.get_namespace(i, j), parents=('Data', f'{sets.name} ({g.title})'))

        return self.namespace

    @QtCore.pyqtSlot(list, list, bool)
    def eval_expression(self, cmds: list, set_ids: list, overwrite: bool):
        ns = self.namespace.flatten()

        if overwrite:
            self.undostack.beginMacro('Evaluate expression')

        failures = []
        for sid in set_ids:
            data_i = self.data[sid]
            try:
                # use a copy of original namespace
                new_data = data_i.eval_expression(cmds, dict(ns))
                if overwrite:
                    cmd = EvalCommand(self.data, sid, new_data, 'Evaluate expression')
                    self.undostack.push(cmd)
                else:
                    new_id = self.copy_sets(sets=[sid])
                    self.data[new_id[0]].data = new_data
            except Exception as e:
                failures.append((data_i, e))
                logger.warning(str(data_i) + ' failed with Exception: ' + ''.join(e.args))
                continue

        if overwrite:
            self.undostack.endMacro()

        if failures:
            err_msg = QtWidgets.QMessageBox(parent=self.sender())
            err_msg.setText('One or more errors occured during evaluation.')
            err_msg.setDetailedText('\n'.join(f'{d.name} failed with error: {err.args}' for d, err in failures))
            err_msg.exec()

        self.sender().success = not failures
        self.sender().add_data(self.active_sets)

    @QtCore.pyqtSlot(list, dict)
    def create_from_function(self, cmds: list, opts: dict):
        ns = dict(self.namespace.flatten())

        dtype = [Points, FID, Spectrum, BDS][opts.pop('dtype')]

        try:
            for c in cmds:
                exec(c, globals(), ns)

            name = opts.pop('name')
            value = opts.pop('val')
            graph = opts.pop('graph')

            data = dtype(x=ns['x'], y=ns['y'], y_err=ns['y_err'], name=name, value=value)
            s_id = self.add(data, **opts)
            self.sender().success = True
            self.newData.emit([s_id], graph)

        except Exception as err:
            logger.exception('Creation failed with error: ' + ', '.join(err.args))
            err_msg = QtWidgets.QMessageBox(parent=self.sender())
            err_msg.setText('One or more errors occurred during evaluation.')
            err_msg.setDetailedText('Creation failed with error: ' + ', '.join(err.args))
            err_msg.exec()

            self.sender().success = False

    def show_statistics(self, mode):
        x, y, = [], []

        for i, _ in self.active_sets:
            _temp = self.data[i]
            try:
                x.append(float(_temp.name))
            except ValueError:
                x.append(i)
            y.append(_temp.statistic(mode))

    @QtCore.pyqtSlot()
    def calc_magn(self):
        new_id = []
        for k, _ in self.active_sets:
            dataset = self.data[k]
            if isinstance(dataset, SignalContainer):
                new_value = dataset.copy(full=True)
                new_value.data = dataset.data.magnitude()
                new_id.append(self.add(new_value))

        self.newData.emit(new_id, '')

    @QtCore.pyqtSlot()
    def center(self):
        new_id = []
        for k, _ in self.active_sets:
            new_value = self.data[k].copy(full=True)
            new_value.x -= new_value.x[np.argmax(new_value.y.real)]
            new_id.append(self.add(new_value))

        self.newData.emit(new_id, '')

    def integrate(self, **kwargs):
        new_sets = []
        log = kwargs['log']
        limits = kwargs.get('limits')
        mode = kwargs['mode']

        for set_id in kwargs['sets']:
            data_i = self.data[set_id]
            if mode == 'i':
                new_data = data_i.data.integrate(log=log, limits=limits)
            elif mode == 'd':
                new_data = data_i.data.diff(log=log)
            else:
                raise ValueError(f'Unknown mode {mode}.')

            new_container = data_i.copy(full=True)
            new_container.data = new_data

            new_sets.append(self.add(new_container))

        self.newData.emit(new_sets, kwargs['graph'])

    def integral_datasets(self, ranges: list, x_vals: list, y_vals: np.ndarry):
        new_sets = []
        for range_i, y_val_i in zip(ranges, y_vals):
            new_sets.append(self.add(Points(x=x_vals, y=y_val_i, name=f'{range_i[0]:.4g}-{range_i[1]:.4g}')))

        self.newData.emit(new_sets, '')

    def bds_deriv(self):
        new_sets = []

        for (set_id, _) in self.active_sets:
            data_i = self.data[set_id]
            diff = data_i.data.diff(log=True)
            new_data = Points(x=diff.x, y=-np.pi/2*diff.y.real)
            new_data.update(data_i.data.meta)

            new_sets.append(self.add(new_data, color=data_i.plot_imag.linecolor))

        self.newData.emit(new_sets, '')

    def logft(self, **kwargs):
        new_sets = []
        ft_mode = kwargs['ft_mode']

        for set_id in kwargs['sets']:
            data_i = self.data[set_id]
            if ft_mode in ['cos', 'sin']:
                new_data = Points(*logft(data_i.x, data_i.y, mode=ft_mode))
            else:
                new_data = Signal(*logft(data_i.x, data_i.y, mode=ft_mode))

            new_sets.append(self.add(new_data, color=data_i['color'], symbol=data_i['symbol'], line=data_i['line']))
            self.data[new_sets[-1]].update(data_i.data.meta)

        self.newData.emit(new_sets, kwargs['graph'])

    def skip_points(self, offset: int, step: int, invert: bool = False, copy: bool = False):
        for k, _ in self.active_sets:
            src = self.data[k]
            if invert:
                mask = np.mod(np.arange(offset, src.x.size+offset), step) != 0
            else:
                mask = np.mod(np.arange(offset, src.x.size+offset), step) == 0

            if copy:
                data = src.copy()
                temp = data.mask.copy()
                temp[temp] = mask

                data.remove(np.where(~temp))
                data.mask = np.ones(data.x.shape)

                idd = self.add(data)
                self.newData.emit([idd], self.current_graph)
            else:
                src.mask[src.mask] = mask
                src.mask = src.mask

    @QtCore.pyqtSlot(dict)
    def calc_relaxation(self, opts: dict):
        params = opts['pts']
        if len(params) == 4:
            if params[3]:
                _x = x1 = np.geomspace(params[0], params[1], num=params[2])
            else:
                _x = x1 = np.linspace(params[0], params[1], num=params[2])

            if opts['axis1'] in ['t', 'invt1000']:
                t_p = opts['t_param']
                if len(t_p) == 2:
                    from nmreval.models import Arrhenius as Func
                else:
                    from nmreval.models import VFT as Func

                _x = Func.func(x1, *t_p, invt=opts['axis1'])

        else:
            if params[1]:
                x1 = self.data[params[0]].x
                _x = self.data[params[0]].y.real
            else:
                _x = x1 = self.data[params[0]].x

        x2 = opts['val2']

        sd = opts['spec_dens']
        sd_param = [self.data[p].y.real if isinstance(p, str) else p for p in opts['sd_param'][0]]
        sd.convert(_x, *sd_param, from_=opts['tau_type'], to_='raw')

        relax = Relaxation()
        relax.set_distribution(sd, parameter=sd_param, keywords=opts['sd_param'][1])

        cp_param = [self.data[p].y.real if isinstance(p, str) else p for p in opts['cp_param'][0]]
        relax.set_coupling(opts['coup'], parameter=cp_param, keywords=opts['cp_param'][1])

        if opts['out'] == 't1':
            y = relax.t1(x2, _x)
        else:
            y = relax.t2(x2, _x)

        pts = Points(x1, y, name=sd.name)
        pts.meta.update(opts)

        # we do not want class instances
        pts.meta['coup'] = opts['coup'].name
        pts.meta['spec_dens'] = sd.name

        self.newData.emit([self.add(pts)], opts['graph'])
        self.sender().update_graphs(self.graphs.list())

    @QtCore.pyqtSlot(str, list)
    def mask_value(self, idx: str, m: list):
        self.data[idx].mask = m

    @QtCore.pyqtSlot(str, list)
    def remove_values(self, idx: str, m: list):
        self.data[idx].remove(m)

    @QtCore.pyqtSlot(str, int)
    def split_set(self, idx: str, row: int):
        selected_data = self.data[idx]
        popular_front_of_judea = selected_data.copy(full=True)

        selected_data.remove(slice(row, None))
        popular_front_of_judea.remove(slice(None, row))

        new_id = self.add(popular_front_of_judea)
        self.newData.emit([new_id], selected_data.graph)

    def set_values(self, idx: str, pos: tuple, value):
        self.data[idx].setvalues(pos, value)

    def append(self, idx: str):
        self.data[idx].add([0.0, 0.0, 0.0])

    def save(self, outpath: str | pathlib.Path, extension: str, strip_spaces=False):
        path = pathlib.Path(outpath)
        suffix = path.suffix

        if not suffix:
            m = re.match(r'[\w\s]*\(\*(\.\w+)\)', extension)
            if m:
                suffix = m.group(1)
                path = path.with_suffix(suffix)
            else:
                raise ValueError('No file extension detected')

        if suffix == '.nmr':
            from nmreval.io.sessionwriter import NMRWriter
            NMRWriter(self.graphs, self.data).export(path)

            return

        real_outnames = []
        for set_id, set_name in self.active_sets:
            full_name = path.stem
            if '<label>' in full_name:
                full_name = full_name.replace('<label>', convert(set_name, old='tex', new='str'))

            data_i = self.data[set_id]

            if isinstance(data_i, FitContainer):
                try:
                    full_name += ' fit(' + self.data[data_i.parent_set].name + ')'
                except KeyError:
                    # TODO fits should have a parent set
                    logger.warning(f'Fit {data_i} without valid parent : key is [{data_i.parent_set}')
                    full_name += ' fit'

            if strip_spaces:
                full_name = full_name.replace(' ', '_')

            if full_name in real_outnames:
                cnt = 1
                while (full_name + '_' + str(cnt)) in real_outnames:
                    cnt += 1
                real_outnames.append(full_name + '_' + str(cnt))
            else:
                real_outnames.append(full_name)

            out_name = real_outnames[-1]
            bad_character = r'/*<>\|:"'
            for c in bad_character:
                out_name = out_name.replace(c, '')

            outpath_set = path.with_name(out_name+path.suffix)
            data_i.save(outpath_set)


class FitWorker(QtCore.QObject):
    finished = QtCore.pyqtSignal(list, bool)

    def __init__(self, fitter, mode):
        super().__init__()

        self.fitter = fitter
        self.mode = mode

    @QtCore.pyqtSlot()
    def run(self):
        try:
            res = self.fitter.run(mode=self.mode)
            success = True
        except Exception as e:
            res = [e]
            success = False
        self.finished.emit(res, success)