grid_based_searches.py

""" Searches using grid-based methods """
from __future__ import division, absolute_import, print_function

import os
import logging
import itertools
from collections import OrderedDict
import datetime
import getpass
import socket

import numpy as np
import matplotlib
import matplotlib.pyplot as plt
from scipy.misc import logsumexp

import pyfstat.helper_functions as helper_functions
from pyfstat.core import (BaseSearchClass, ComputeFstat,
                          SemiCoherentGlitchSearch, SemiCoherentSearch, tqdm,
                          args, read_par)
import lalpulsar
import lal


class GridSearch(BaseSearchClass):
    """ Gridded search using ComputeFstat """
    tex_labels = {'F0': '$f$', 'F1': '$\dot{f}$', 'F2': '$\ddot{f}$',
                  'Alpha': r'$\alpha$', 'Delta': r'$\delta$'}
    tex_labels0 = {'F0': '$-f_0$', 'F1': '$-\dot{f}_0$', 'F2': '$-\ddot{f}_0$',
                   'Alpha': r'$-\alpha_0$', 'Delta': r'$-\delta_0$'}

    @helper_functions.initializer
    def __init__(self, label, outdir, sftfilepattern, F0s, F1s, F2s, Alphas,
                 Deltas, tref=None, minStartTime=None, maxStartTime=None,
                 nsegs=1, BSGL=False, minCoverFreq=None, maxCoverFreq=None,
                 detectors=None, SSBprec=None, injectSources=None,
                 input_arrays=False, assumeSqrtSX=None):
        """
        Parameters
        ----------
        label, outdir: str
            A label and directory to read/write data from/to
        sftfilepattern: str
            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
            mutiple patterns can be given separated by colons.
        F0s, F1s, F2s, delta_F0s, delta_F1s, tglitchs, Alphas, Deltas: tuple
            Length 3 tuple describing the grid for each parameter, e.g
            [F0min, F0max, dF0], for a fixed value simply give [F0]. Unless
            input_arrays == True, then these are the values to search at.
        tref, minStartTime, maxStartTime: int
            GPS seconds of the reference time, start time and end time
        input_arrays: bool
            if true, use the F0s, F1s, etc as is

        For all other parameters, see `pyfstat.ComputeFStat` for details
        """

        if os.path.isdir(outdir) is False:
            os.mkdir(outdir)
        self.set_out_file()
        self.keys = ['_', '_', 'F0', 'F1', 'F2', 'Alpha', 'Delta']
        self.search_keys = [x+'s' for x in self.keys[2:]]
        for k in self.search_keys:
            setattr(self, k, np.atleast_1d(getattr(self, k)))

    def inititate_search_object(self):
        logging.info('Setting up search object')
        if self.nsegs == 1:
            self.search = ComputeFstat(
                tref=self.tref, sftfilepattern=self.sftfilepattern,
                minCoverFreq=self.minCoverFreq, maxCoverFreq=self.maxCoverFreq,
                detectors=self.detectors,
                minStartTime=self.minStartTime, maxStartTime=self.maxStartTime,
                BSGL=self.BSGL, SSBprec=self.SSBprec,
                injectSources=self.injectSources,
                assumeSqrtSX=self.assumeSqrtSX)
            self.search.get_det_stat = self.search.get_fullycoherent_twoF
        else:
            self.search = SemiCoherentSearch(
                label=self.label, outdir=self.outdir, tref=self.tref,
                nsegs=self.nsegs, sftfilepattern=self.sftfilepattern,
                BSGL=self.BSGL, minStartTime=self.minStartTime,
                maxStartTime=self.maxStartTime, minCoverFreq=self.minCoverFreq,
                maxCoverFreq=self.maxCoverFreq, detectors=self.detectors,
                injectSources=self.injectSources)

            def cut_out_tstart_tend(*vals):
                return self.search.get_semicoherent_twoF(*vals[2:])
            self.search.get_det_stat = cut_out_tstart_tend

    def get_array_from_tuple(self, x):
        if len(x) == 1:
            return np.array(x)
        elif len(x) == 3 and self.input_arrays is False:
            return np.arange(x[0], x[1], x[2])
        else:
            logging.info('Using tuple as is')
            return np.array(x)

    def get_input_data_array(self):
        logging.info("Generating input data array")
        coord_arrays = []
        for tup in ([self.minStartTime], [self.maxStartTime], self.F0s,
                    self.F1s, self.F2s, self.Alphas, self.Deltas):
            coord_arrays.append(self.get_array_from_tuple(tup))

        input_data = []
        for vals in itertools.product(*coord_arrays):
                input_data.append(vals)
        self.input_data = np.array(input_data)
        self.coord_arrays = coord_arrays

    def check_old_data_is_okay_to_use(self):
        if args.clean:
            return False
        if os.path.isfile(self.out_file) is False:
            logging.info(
                'No old data found in "{:s}", continuing with grid search'
                .format(self.out_file))
            return False
        if self.sftfilepattern is not None:
            oldest_sft = min([os.path.getmtime(f) for f in
                              self._get_list_of_matching_sfts()])
            if os.path.getmtime(self.out_file) < oldest_sft:
                logging.info('Search output data outdates sft files,'
                             + ' continuing with grid search')
                return False

        data = np.atleast_2d(np.genfromtxt(self.out_file, delimiter=' '))
        if np.all(data[:, 0: len(self.coord_arrays)] ==
                  self.input_data[:, 0:len(self.coord_arrays)]):
            logging.info(
                'Old data found in "{:s}" with matching input, no search '
                'performed'.format(self.out_file))
            return data
        else:
            logging.info(
                'Old data found in "{:s}", input differs, continuing with '
                'grid search'.format(self.out_file))
            return False
        return False

    def run(self, return_data=False):
        self.get_input_data_array()
        old_data = self.check_old_data_is_okay_to_use()
        if old_data is not False:
            self.data = old_data
            return

        if hasattr(self, 'search') is False:
            self.inititate_search_object()

        data = []
        for vals in tqdm(self.input_data):
            detstat = self.search.get_det_stat(*vals)
            thisCand = list(vals) + [detstat]
            data.append(thisCand)

        data = np.array(data, dtype=np.float)
        if return_data:
            return data
        else:
            self.save_array_to_disk(data)
            self.data = data

    def get_header(self):
        header = ';'.join(['date:{}'.format(str(datetime.datetime.now())),
                           'user:{}'.format(getpass.getuser()),
                           'hostname:{}'.format(socket.gethostname())])
        header += '\n' + ' '.join(self.keys)
        return header

    def save_array_to_disk(self, data):
        logging.info('Saving data to {}'.format(self.out_file))
        header = self.get_header()
        np.savetxt(self.out_file, data, delimiter=' ', header=header)

    def convert_F0_to_mismatch(self, F0, F0hat, Tseg):
        DeltaF0 = F0[1] - F0[0]
        m_spacing = (np.pi*Tseg*DeltaF0)**2 / 12.
        N = len(F0)
        return np.arange(-N*m_spacing/2., N*m_spacing/2., m_spacing)

    def convert_F1_to_mismatch(self, F1, F1hat, Tseg):
        DeltaF1 = F1[1] - F1[0]
        m_spacing = (np.pi*Tseg**2*DeltaF1)**2 / 720.
        N = len(F1)
        return np.arange(-N*m_spacing/2., N*m_spacing/2., m_spacing)

    def add_mismatch_to_ax(self, ax, x, y, xkey, ykey, xhat, yhat, Tseg):
        axX = ax.twiny()
        axX.zorder = -10
        axY = ax.twinx()
        axY.zorder = -10

        if xkey == 'F0':
            m = self.convert_F0_to_mismatch(x, xhat, Tseg)
            axX.set_xlim(m[0], m[-1])

        if ykey == 'F1':
            m = self.convert_F1_to_mismatch(y, yhat, Tseg)
            axY.set_ylim(m[0], m[-1])

    def plot_1D(self, xkey, ax=None, x0=None, xrescale=1, savefig=True,
                xlabel=None, ylabel='$\widetilde{2\mathcal{F}}$'):
        if ax is None:
            fig, ax = plt.subplots()
        xidx = self.keys.index(xkey)
        x = np.unique(self.data[:, xidx])
        if x0:
            x = x - x0
        x = x * xrescale
        z = self.data[:, -1]
        ax.plot(x, z)
        if x0:
            ax.set_xlabel(self.tex_labels[xkey]+self.tex_labels0[xkey])
        else:
            ax.set_xlabel(self.tex_labels[xkey])

        if xlabel:
            ax.set_xlabel(xlabel)

        ax.set_ylabel(ylabel)
        if savefig:
            fig.tight_layout()
            fig.savefig('{}/{}_1D.png'.format(self.outdir, self.label))
        else:
            return ax

    def plot_2D(self, xkey, ykey, ax=None, save=True, vmin=None, vmax=None,
                add_mismatch=None, xN=None, yN=None, flat_keys=[],
                rel_flat_idxs=[], flatten_method=np.max, title=None,
                predicted_twoF=None, cm=None, cbarkwargs={}, x0=None, y0=None,
                colorbar=False):
        """ Plots a 2D grid of 2F values

        Parameters
        ----------
        add_mismatch: tuple (xhat, yhat, Tseg)
            If not None, add a secondary axis with the metric mismatch from the
            point xhat, yhat with duration Tseg
        flatten_method: np.max
            Function to use in flattening the flat_keys
        """
        if ax is None:
            fig, ax = plt.subplots()
        xidx = self.keys.index(xkey)
        yidx = self.keys.index(ykey)
        flat_idxs = [self.keys.index(k) for k in flat_keys]

        x = np.unique(self.data[:, xidx])
        if x0:
            x = x-x0
        y = np.unique(self.data[:, yidx])
        if y0:
            y = y-y0
        flat_vals = [np.unique(self.data[:, j]) for j in flat_idxs]
        z = self.data[:, -1]

        Y, X = np.meshgrid(y, x)
        shape = [len(x), len(y)] + [len(v) for v in flat_vals]
        Z = z.reshape(shape)

        if len(rel_flat_idxs) > 0:
            Z = flatten_method(Z, axis=tuple(rel_flat_idxs))

        if predicted_twoF:
            Z = (predicted_twoF - Z) / (predicted_twoF + 4)
            if cm is None:
                cm = plt.cm.viridis_r
        else:
            if cm is None:
                cm = plt.cm.viridis

        pax = ax.pcolormesh(X, Y, Z, cmap=cm, vmin=vmin, vmax=vmax)
        if colorbar:
            cb = plt.colorbar(pax, ax=ax, **cbarkwargs)
            cb.set_label('$2\mathcal{F}$')

        if add_mismatch:
            self.add_mismatch_to_ax(ax, x, y, xkey, ykey, *add_mismatch)

        ax.set_xlim(x[0], x[-1])
        ax.set_ylim(y[0], y[-1])
        if x0:
            ax.set_xlabel(self.tex_labels[xkey]+self.tex_labels0[xkey])
        else:
            ax.set_xlabel(self.tex_labels[xkey])
        if y0:
            ax.set_ylabel(self.tex_labels[ykey]+self.tex_labels0[ykey])
        else:
            ax.set_ylabel(self.tex_labels[ykey])

        if title:
            ax.set_title(title)

        if xN:
            ax.xaxis.set_major_locator(matplotlib.ticker.MaxNLocator(xN))
        if yN:
            ax.yaxis.set_major_locator(matplotlib.ticker.MaxNLocator(yN))

        if save:
            fig.tight_layout()
            fig.savefig('{}/{}_2D.png'.format(self.outdir, self.label))
        else:
            return ax

    def get_max_twoF(self):
        """ Get the maximum twoF over the grid

        Returns
        -------
        d: dict
            Dictionary containing, 'minStartTime', 'maxStartTime', 'F0', 'F1',
            'F2', 'Alpha', 'Delta' and 'twoF' of maximum

        """

        twoF = self.data[:, -1]
        idx = np.argmax(twoF)
        v = self.data[idx, :]
        d = OrderedDict(minStartTime=v[0], maxStartTime=v[1], F0=v[2], F1=v[3],
                        F2=v[4], Alpha=v[5], Delta=v[6], twoF=v[7])
        return d

    def print_max_twoF(self):
        d = self.get_max_twoF()
        print('Max twoF values for {}:'.format(self.label))
        for k, v in d.iteritems():
            print('  {}={}'.format(k, v))

    def set_out_file(self, extra_label=None):
        if self.detectors:
            dets = self.detectors.replace(',', '')
        else:
            dets = 'NA'
        if extra_label:
            self.out_file = '{}/{}_{}_{}_{}.txt'.format(
                self.outdir, self.label, dets, type(self).__name__,
                extra_label)
        else:
            self.out_file = '{}/{}_{}_{}.txt'.format(
                self.outdir, self.label, dets, type(self).__name__)


class TransientGridSearch(GridSearch):
    """ Gridded transient-continous search using ComputeFstat """

    @helper_functions.initializer
    def __init__(self, label, outdir, sftfilepattern, F0s, F1s, F2s, Alphas,
                 Deltas, tref=None, minStartTime=None, maxStartTime=None,
                 BSGL=False, minCoverFreq=None, maxCoverFreq=None,
                 detectors=None, SSBprec=None, injectSources=None,
                 input_arrays=False, assumeSqrtSX=None,
                 transientWindowType=None, t0Band=None, tauBand=None,
                 dt0=None, dtau=None,
                 outputTransientFstatMap=False):
        """
        Parameters
        ----------
        label, outdir: str
            A label and directory to read/write data from/to
        sftfilepattern: str
            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
            mutiple patterns can be given separated by colons.
        F0s, F1s, F2s, delta_F0s, delta_F1s, tglitchs, Alphas, Deltas: tuple
            Length 3 tuple describing the grid for each parameter, e.g
            [F0min, F0max, dF0], for a fixed value simply give [F0]. Unless
            input_arrays == True, then these are the values to search at.
        tref, minStartTime, maxStartTime: int
            GPS seconds of the reference time, start time and end time
        input_arrays: bool
            if true, use the F0s, F1s, etc as is
        transientWindowType: str
            If 'rect' or 'exp', compute atoms so that a transient (t0,tau) map
            can later be computed.  ('none' instead of None explicitly calls
            the transient-window function, but with the full range, for
            debugging). Currently only supported for nsegs=1.
        t0Band, tauBand: int
            if >0, search t0 in (minStartTime,minStartTime+t0Band)
                   and tau in (2*Tsft,2*Tsft+tauBand).
            if =0, only compute CW Fstat with t0=minStartTime,
                   tau=maxStartTime-minStartTime.
        dt0, dtau: int
            grid resolutions in transient start-time and duration,
            both default to Tsft
        outputTransientFstatMap: bool
            if true, write output files for (t0,tau) Fstat maps
            (one file for each doppler grid point!)

        For all other parameters, see `pyfstat.ComputeFStat` for details
        """

        self.nsegs = 1
        if os.path.isdir(outdir) is False:
            os.mkdir(outdir)
        self.set_out_file()
        self.keys = ['_', '_', 'F0', 'F1', 'F2', 'Alpha', 'Delta']
        self.search_keys = [x+'s' for x in self.keys[2:]]
        for k in self.search_keys:
            setattr(self, k, np.atleast_1d(getattr(self, k)))

    def inititate_search_object(self):
        logging.info('Setting up search object')
        self.search = ComputeFstat(
            tref=self.tref, sftfilepattern=self.sftfilepattern,
            minCoverFreq=self.minCoverFreq, maxCoverFreq=self.maxCoverFreq,
            detectors=self.detectors,
            transientWindowType=self.transientWindowType,
            t0Band=self.t0Band, tauBand=self.tauBand,
            dt0=self.dt0, dtau=self.dtau,
            minStartTime=self.minStartTime, maxStartTime=self.maxStartTime,
            BSGL=self.BSGL, SSBprec=self.SSBprec,
            injectSources=self.injectSources,
            assumeSqrtSX=self.assumeSqrtSX)
        self.search.get_det_stat = self.search.get_fullycoherent_twoF

    def run(self, return_data=False):
        self.get_input_data_array()
        old_data = self.check_old_data_is_okay_to_use()
        if old_data is not False:
            self.data = old_data
            return

        if hasattr(self, 'search') is False:
            self.inititate_search_object()

        data = []
        for vals in tqdm(self.input_data):
            detstat = self.search.get_det_stat(*vals)
            windowRange = getattr(self.search, 'windowRange', None)
            FstatMap = getattr(self.search, 'FstatMap', None)
            thisCand = list(vals) + [detstat]
            if getattr(self, 'transientWindowType', None):
                if self.outputTransientFstatMap:
                    tCWfile = os.path.splitext(self.out_file)[0]+'_tCW_%.16f_%.16f_%.16f_%.16g_%.16g.dat' % (vals[2],vals[5],vals[6],vals[3],vals[4]) # freq alpha delta f1dot f2dot
                    fo = lal.FileOpen(tCWfile, 'w')
                    lalpulsar.write_transientFstatMap_to_fp ( fo, FstatMap, windowRange, None )
                    del fo # instead of lal.FileClose() which is not SWIG-exported
                Fmn = FstatMap.F_mn.data
                maxidx = np.unravel_index(Fmn.argmax(), Fmn.shape)
                thisCand += [windowRange.t0+maxidx[0]*windowRange.dt0,
                             windowRange.tau+maxidx[1]*windowRange.dtau]
            data.append(thisCand)

        data = np.array(data, dtype=np.float)
        if return_data:
            return data
        else:
            self.save_array_to_disk(data)
            self.data = data


class SliceGridSearch(GridSearch):
    """ Slice gridded search using ComputeFstat """
    @helper_functions.initializer
    def __init__(self, label, outdir, sftfilepattern, F0s, F1s, F2s, Alphas,
                 Deltas, tref=None, minStartTime=None, maxStartTime=None,
                 nsegs=1, BSGL=False, minCoverFreq=None, maxCoverFreq=None,
                 detectors=None, SSBprec=None, injectSources=None,
                 input_arrays=False, assumeSqrtSX=None, Lambda0=None):
        """
        Parameters
        ----------
        label, outdir: str
            A label and directory to read/write data from/to
        sftfilepattern: str
            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
            mutiple patterns can be given separated by colons.
        F0s, F1s, F2s, delta_F0s, delta_F1s, tglitchs, Alphas, Deltas: tuple
            Length 3 tuple describing the grid for each parameter, e.g
            [F0min, F0max, dF0], for a fixed value simply give [F0]. Unless
            input_arrays == True, then these are the values to search at.
        tref, minStartTime, maxStartTime: int
            GPS seconds of the reference time, start time and end time
        input_arrays: bool
            if true, use the F0s, F1s, etc as is

        For all other parameters, see `pyfstat.ComputeFStat` for details
        """

        if os.path.isdir(outdir) is False:
            os.mkdir(outdir)
        self.set_out_file()
        self.keys = ['_', '_', 'F0', 'F1', 'F2', 'Alpha', 'Delta']
        self.ndim = 0
        self.thetas = [F0s, F1s, Alphas, Deltas]
        self.ndim = 4

        self.search_keys = ['F0', 'F1', 'Alpha', 'Delta']
        if self.Lambda0 is None:
            raise ValueError('Lambda0 undefined')
        if len(self.Lambda0) != len(self.search_keys):
            raise ValueError(
                'Lambda0 must be of length {}'.format(len(self.search_keys)))
        self.Lambda0 = np.array(Lambda0)

    def run(self, factor=2, max_n_ticks=4, whspace=0.07, save=True,
            **kwargs):
        lbdim = 0.5 * factor   # size of left/bottom margin
        trdim = 0.4 * factor   # size of top/right margin
        plotdim = factor * self.ndim + factor * (self.ndim - 1.) * whspace
        dim = lbdim + plotdim + trdim

        fig, axes = plt.subplots(self.ndim, self.ndim, figsize=(dim, dim))

        # Format the figure.
        lb = lbdim / dim
        tr = (lbdim + plotdim) / dim
        fig.subplots_adjust(left=lb, bottom=lb, right=tr, top=tr,
                            wspace=whspace, hspace=whspace)

        search = GridSearch(
            self.label, self.outdir, self.sftfilepattern,
            F0s=self.Lambda0[0], F1s=self.Lambda0[1], F2s=self.F2s[0],
            Alphas=self.Lambda0[2], Deltas=self.Lambda0[3], tref=self.tref,
            minStartTime=self.minStartTime, maxStartTime=self.maxStartTime)

        for i, ikey in enumerate(self.search_keys):
            setattr(search, ikey+'s', self.thetas[i])
            search.label = '{}_{}'.format(self.label, ikey)
            search.set_out_file()
            search.run()
            axes[i, i] = search.plot_1D(ikey, ax=axes[i, i], savefig=False,
                                        x0=self.Lambda0[i]
                                        )
            setattr(search, ikey+'s', [self.Lambda0[i]])
            axes[i, i].yaxis.tick_right()
            axes[i, i].yaxis.set_label_position("right")
            axes[i, i].set_xlabel('')

            for j, jkey in enumerate(self.search_keys):
                ax = axes[i, j]

                if j > i:
                    ax.set_frame_on(False)
                    ax.set_xticks([])
                    ax.set_yticks([])
                    continue

                ax.get_shared_x_axes().join(axes[self.ndim-1, j], ax)
                if i < self.ndim - 1:
                    ax.set_xticklabels([])
                if j < i:
                    ax.get_shared_y_axes().join(axes[i, i-1], ax)
                    if j > 0:
                        ax.set_yticklabels([])
                if j == i:
                    continue

                ax.xaxis.set_major_locator(
                    matplotlib.ticker.MaxNLocator(max_n_ticks, prune="upper"))
                ax.yaxis.set_major_locator(
                    matplotlib.ticker.MaxNLocator(max_n_ticks, prune="upper"))

                setattr(search, ikey+'s', self.thetas[i])
                setattr(search, jkey+'s', self.thetas[j])
                search.label = '{}_{}'.format(self.label, ikey+jkey)
                search.set_out_file()
                search.run()
                ax = search.plot_2D(jkey, ikey, ax=ax, save=False,
                                    y0=self.Lambda0[i], x0=self.Lambda0[j],
                                    **kwargs)
                setattr(search, ikey+'s', [self.Lambda0[i]])
                setattr(search, jkey+'s', [self.Lambda0[j]])

                ax.grid(lw=0.2, ls='--', zorder=10)
                ax.set_xlabel('')
                ax.set_ylabel('')

        for i, ikey in enumerate(self.search_keys):
            axes[-1, i].set_xlabel(
                self.tex_labels[ikey]+self.tex_labels0[ikey])
            if i > 0:
                axes[i, 0].set_ylabel(
                    self.tex_labels[ikey]+self.tex_labels0[ikey])
            axes[i, i].set_ylabel("$2\mathcal{F}$")

        if save:
            fig.savefig(
                '{}/{}_slice_projection.png'.format(self.outdir, self.label))
        else:
            return fig, axes


class GridUniformPriorSearch():
    @helper_functions.initializer
    def __init__(self, theta_prior, NF0, NF1, label, outdir, sftfilepattern,
                 tref, minStartTime, maxStartTime, minCoverFreq=None,
                 maxCoverFreq=None, BSGL=False, detectors=None, nsegs=1,
                 SSBprec=None, injectSources=None):
        dF0 = (theta_prior['F0']['upper'] - theta_prior['F0']['lower'])/NF0
        dF1 = (theta_prior['F1']['upper'] - theta_prior['F1']['lower'])/NF1
        F0s = [theta_prior['F0']['lower'], theta_prior['F0']['upper'], dF0]
        F1s = [theta_prior['F1']['lower'], theta_prior['F1']['upper'], dF1]
        self.search = GridSearch(
            label, outdir, sftfilepattern, F0s=F0s, F1s=F1s, tref=tref,
            Alphas=[theta_prior['Alpha']], Deltas=[theta_prior['Delta']],
            minStartTime=minStartTime, maxStartTime=maxStartTime, BSGL=BSGL,
            detectors=detectors, minCoverFreq=minCoverFreq,
            injectSources=injectSources, maxCoverFreq=maxCoverFreq,
            nsegs=nsegs, SSBprec=SSBprec)

    def run(self):
        self.search.run()

    def get_2D_plot(self, **kwargs):
        return self.search.plot_2D('F0', 'F1', **kwargs)


class GridGlitchSearch(GridSearch):
    """ Grid search using the SemiCoherentGlitchSearch """
    @helper_functions.initializer
    def __init__(self, label, outdir='data', sftfilepattern=None, F0s=[0],
                 F1s=[0], F2s=[0], delta_F0s=[0], delta_F1s=[0], tglitchs=None,
                 Alphas=[0], Deltas=[0], tref=None, minStartTime=None,
                 maxStartTime=None, minCoverFreq=None, maxCoverFreq=None,
                 detectors=None):
        """
        Run a single-glitch grid search

        Parameters
        ----------
        label, outdir: str
            A label and directory to read/write data from/to
        sftfilepattern: str
            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
            mutiple patterns can be given separated by colons.
        F0s, F1s, F2s, delta_F0s, delta_F1s, tglitchs, Alphas, Deltas: tuple
            Length 3 tuple describing the grid for each parameter, e.g
            [F0min, F0max, dF0], for a fixed value simply give [F0]. Note that
            tglitchs is referenced to zero at minStartTime.
        tref, minStartTime, maxStartTime: int
            GPS seconds of the reference time, start time and end time

        For all other parameters, see pyfstat.ComputeFStat.
        """

        self.BSGL = False
        self.input_arrays = False
        if tglitchs is None:
            raise ValueError('You must specify `tglitchs`')

        self.search = SemiCoherentGlitchSearch(
            label=label, outdir=outdir, sftfilepattern=self.sftfilepattern,
            tref=tref, minStartTime=minStartTime, maxStartTime=maxStartTime,
            minCoverFreq=minCoverFreq, maxCoverFreq=maxCoverFreq,
            BSGL=self.BSGL)
        self.search.get_det_stat = self.search.get_semicoherent_nglitch_twoF

        if os.path.isdir(outdir) is False:
            os.mkdir(outdir)
        self.set_out_file()
        self.keys = ['F0', 'F1', 'F2', 'Alpha', 'Delta', 'delta_F0',
                     'delta_F1', 'tglitch']

    def get_input_data_array(self):
        logging.info("Generating input data array")
        coord_arrays = []
        for tup in (self.F0s, self.F1s, self.F2s, self.Alphas, self.Deltas,
                    self.delta_F0s, self.delta_F1s, self.tglitchs):
            coord_arrays.append(self.get_array_from_tuple(tup))

        input_data = []
        for vals in itertools.product(*coord_arrays):
            input_data.append(vals)
        self.input_data = np.array(input_data)
        self.coord_arrays = coord_arrays


class FrequencySlidingWindow(GridSearch):
    """ A sliding-window search over the Frequency """
    @helper_functions.initializer
    def __init__(self, label, outdir, sftfilepattern, F0s, F1, F2,
                 Alpha, Delta, tref, minStartTime=None,
                 maxStartTime=None, window_size=10*86400, window_delta=86400,
                 BSGL=False, minCoverFreq=None, maxCoverFreq=None,
                 detectors=None, SSBprec=None, injectSources=None):
        """
        Parameters
        ----------
        label, outdir: str
            A label and directory to read/write data from/to
        sftfilepattern: str
            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
            mutiple patterns can be given separated by colons.
        F0s: array
            Frequency range
        F1, F2, Alpha, Delta: float
            Fixed values to compute twoF(F) over
        tref, minStartTime, maxStartTime: int
            GPS seconds of the reference time, start time and end time

        For all other parameters, see `pyfstat.ComputeFStat` for details
        """

        self.transientWindowType = None
        self.t0Band = None
        self.tauBand = None

        if os.path.isdir(outdir) is False:
            os.mkdir(outdir)
        self.set_out_file()
        self.nsegs = 1
        self.F1s = [F1]
        self.F2s = [F2]
        self.Alphas = [Alpha]
        self.Deltas = [Delta]
        self.input_arrays = False
        self.keys = ['_', '_', 'F0', 'F1', 'F2', 'Alpha', 'Delta']

    def inititate_search_object(self):
        logging.info('Setting up search object')
        self.search = ComputeFstat(
            tref=self.tref, sftfilepattern=self.sftfilepattern,
            minCoverFreq=self.minCoverFreq, maxCoverFreq=self.maxCoverFreq,
            detectors=self.detectors, transientWindowType=self.transientWindowType,
            minStartTime=self.minStartTime, maxStartTime=self.maxStartTime,
            BSGL=self.BSGL, SSBprec=self.SSBprec,
            injectSources=self.injectSources)
        self.search.get_det_stat = (
            self.search.get_fullycoherent_twoF)

    def get_input_data_array(self):
        arrays = []
        tstarts = [self.minStartTime]
        while tstarts[-1] + self.window_size < self.maxStartTime:
            tstarts.append(tstarts[-1]+self.window_delta)
        arrays = [tstarts]
        for tup in (self.F0s, self.F1s, self.F2s,
                    self.Alphas, self.Deltas):
            arrays.append(self.get_array_from_tuple(tup))

        input_data = []
        for vals in itertools.product(*arrays):
            input_data.append(vals)

        input_data = np.array(input_data)
        input_data = np.insert(
            input_data, 1, input_data[:, 0] + self.window_size, axis=1)

        self.arrays = arrays
        self.input_data = np.array(input_data)

    def plot_sliding_window(self, F0=None, ax=None, savefig=True,
                            colorbar=True, timestamps=False):
        data = self.data
        if ax is None:
            ax = plt.subplot()
        tstarts = np.unique(data[:, 0])
        tends = np.unique(data[:, 1])
        frequencies = np.unique(data[:, 2])
        twoF = data[:, -1]
        tmids = (tstarts + tends) / 2.0
        dts = (tmids - self.minStartTime) / 86400.
        if F0:
            frequencies = frequencies - F0
            ax.set_ylabel('Frequency - $f_0$ [Hz] \n $f_0={:0.2f}$'.format(F0))
        else:
            ax.set_ylabel('Frequency [Hz]')
        twoF = twoF.reshape((len(tmids), len(frequencies)))
        Y, X = np.meshgrid(frequencies, dts)
        pax = ax.pcolormesh(X, Y, twoF)
        if colorbar:
            cb = plt.colorbar(pax, ax=ax)
            cb.set_label('$2\mathcal{F}$')
        ax.set_xlabel(
            r'Mid-point (days after $t_\mathrm{{start}}$={})'.format(
                self.minStartTime))
        ax.set_title(
            'Sliding window length = {} days in increments of {} days'
            .format(self.window_size/86400, self.window_delta/86400),
            )
        if timestamps:
            axT = ax.twiny()
            axT.set_xlim(tmids[0]*1e-9, tmids[-1]*1e-9)
            axT.set_xlabel('Mid-point timestamp [GPS $10^{9}$ s]')
            ax.set_title(ax.get_title(), y=1.18)
        if savefig:
            plt.tight_layout()
            plt.savefig(
                '{}/{}_sliding_window.png'.format(self.outdir, self.label))
        else:
            return ax


class EarthTest(GridSearch):
    """ """
    tex_labels = {'deltaRadius': '$\Delta R$ [m]',
                  'phaseOffset': 'phase-offset [rad]',
                  'deltaPspin': '$\Delta P_\mathrm{spin}$ [s]'}

    @helper_functions.initializer
    def __init__(self, label, outdir, sftfilepattern, deltaRadius,
                 phaseOffset, deltaPspin, F0, F1, F2, Alpha,
                 Delta, tref=None, minStartTime=None, maxStartTime=None,
                 BSGL=False, minCoverFreq=None, maxCoverFreq=None,
                 detectors=None, injectSources=None,
                 assumeSqrtSX=None):
        """
        Parameters
        ----------
        label, outdir: str
            A label and directory to read/write data from/to
        sftfilepattern: str
            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
            mutiple patterns can be given separated by colons.
        F0, F1, F2, Alpha, Delta: float
        tref, minStartTime, maxStartTime: int
            GPS seconds of the reference time, start time and end time

        For all other parameters, see `pyfstat.ComputeFStat` for details
        """
        self.transientWindowType = None
        self.t0Band = None
        self.tauBand = None

        if os.path.isdir(outdir) is False:
            os.mkdir(outdir)
        self.nsegs = 1
        self.F0s = [F0]
        self.F1s = [F1]
        self.F2s = [F2]
        self.Alphas = [Alpha]
        self.Deltas = [Delta]
        self.duration = maxStartTime - minStartTime
        self.deltaRadius = np.atleast_1d(deltaRadius)
        self.phaseOffset = np.atleast_1d(phaseOffset)
        self.phaseOffset = self.phaseOffset + 1e-12  # Hack to stop cached data being used
        self.deltaPspin = np.atleast_1d(deltaPspin)
        self.set_out_file()
        self.SSBprec = lalpulsar.SSBPREC_RELATIVISTIC
        self.keys = ['deltaRadius', 'phaseOffset', 'deltaPspin']

        self.prior_widths = [
            np.max(self.deltaRadius)-np.min(self.deltaRadius),
            np.max(self.phaseOffset)-np.min(self.phaseOffset),
            np.max(self.deltaPspin)-np.min(self.deltaPspin)]

        if hasattr(self, 'search') is False:
            self.inititate_search_object()

    def get_input_data_array(self):
        logging.info("Generating input data array")
        coord_arrays = [self.deltaRadius, self.phaseOffset, self.deltaPspin]
        input_data = []
        for vals in itertools.product(*coord_arrays):
                input_data.append(vals)
        self.input_data = np.array(input_data)
        self.coord_arrays = coord_arrays

    def run_special(self):
        vals = [self.minStartTime, self.maxStartTime, self.F0, self.F1,
                self.F2, self.Alpha, self.Delta]
        self.special_data = {'zero': [0, 0, 0]}
        for key, (dR, dphi, dP) in self.special_data.iteritems():
            rescaleRadius = (1 + dR / lal.REARTH_SI)
            rescalePeriod = (1 + dP / lal.DAYSID_SI)
            lalpulsar.BarycenterModifyEarthRotation(
                rescaleRadius, dphi, rescalePeriod, self.tref)
            FS = self.search.get_det_stat(*vals)
            self.special_data[key] = list([dR, dphi, dP]) + [FS]

    def run(self):
        self.run_special()
        self.get_input_data_array()
        old_data = self.check_old_data_is_okay_to_use()
        if old_data is not False:
            self.data = old_data
            return

        data = []
        vals = [self.minStartTime, self.maxStartTime, self.F0, self.F1,
                self.F2, self.Alpha, self.Delta]
        for (dR, dphi, dP) in tqdm(self.input_data):
            rescaleRadius = (1 + dR / lal.REARTH_SI)
            rescalePeriod = (1 + dP / lal.DAYSID_SI)
            lalpulsar.BarycenterModifyEarthRotation(
                rescaleRadius, dphi, rescalePeriod, self.tref)
            FS = self.search.get_det_stat(*vals)
            data.append(list([dR, dphi, dP]) + [FS])

        data = np.array(data, dtype=np.float)
        logging.info('Saving data to {}'.format(self.out_file))
        np.savetxt(self.out_file, data, delimiter=' ')
        self.data = data

    def marginalised_bayes_factor(self, prior_widths=None):
        if prior_widths is None:
            prior_widths = self.prior_widths

        ndims = self.data.shape[1] - 1
        params = np.array([np.unique(self.data[:, j]) for j in range(ndims)])
        twoF = self.data[:, -1].reshape(tuple([len(p) for p in params]))
        F = twoF / 2.0
        for i, x in enumerate(params[::-1]):
            if len(x) > 1:
                dx = x[1] - x[0]
                F = logsumexp(F, axis=-1)+np.log(dx)-np.log(prior_widths[-1-i])
            else:
                F = np.squeeze(F, axis=-1)
        marginalised_F = np.atleast_1d(F)[0]
        F_at_zero = self.special_data['zero'][-1]/2.0

        max_idx = np.argmax(self.data[:, -1])
        max_F = self.data[max_idx, -1]/2.0
        max_F_params = self.data[max_idx, :-1]
        logging.info('F at zero = {:.1f}, marginalised_F = {:.1f},'
                     ' max_F = {:.1f} ({})'.format(
                         F_at_zero, marginalised_F, max_F, max_F_params))
        return F_at_zero - marginalised_F, (F_at_zero - max_F) / F_at_zero

    def plot_corner(self, prior_widths=None, fig=None, axes=None,
                    projection='log_mean'):
        Bsa, FmaxMismatch = self.marginalised_bayes_factor(prior_widths)

        data = self.data[:, -1].reshape(
            (len(self.deltaRadius), len(self.phaseOffset),
             len(self.deltaPspin)))
        xyz = [self.deltaRadius/lal.REARTH_SI, self.phaseOffset/(np.pi),
               self.deltaPspin/60.]
        labels = [r'$\frac{\Delta R}{R_\mathrm{Earth}}$',
                  r'$\frac{\Delta \phi}{\pi}$',
                  r'$\Delta P_\mathrm{spin}$ [min]',
                  r'$2\mathcal{F}$']

        try:
            from gridcorner import gridcorner
        except ImportError:
            raise ImportError(
                "Python module 'gridcorner' not found, please install from "
                "https://gitlab.aei.uni-hannover.de/GregAshton/gridcorner")

        fig, axes = gridcorner(data, xyz, projection=projection, factor=1.6,
                               labels=labels)
        axes[-1][-1].axvline((lal.DAYJUL_SI - lal.DAYSID_SI)/60.0, color='C3')
        plt.suptitle(
            'T={:.1f} days, $f$={:.2f} Hz, $\log\mathcal{{B}}_{{S/A}}$={:.1f},'
            r' $\frac{{\mathcal{{F}}_0-\mathcal{{F}}_\mathrm{{max}}}}'
            r'{{\mathcal{{F}}_0}}={:.1e}$'
            .format(self.duration/86400, self.F0, Bsa, FmaxMismatch), y=0.99,
            size=14)
        fig.savefig('{}/{}_projection_matrix.png'.format(
            self.outdir, self.label))

    def plot(self, key, prior_widths=None):
        Bsa, FmaxMismatch = self.marginalised_bayes_factor(prior_widths)

        rescales_defaults = {'deltaRadius': 1/lal.REARTH_SI,
                             'phaseOffset': 1/np.pi,
                             'deltaPspin': 1}
        labels = {'deltaRadius': r'$\frac{\Delta R}{R_\mathrm{Earth}}$',
                  'phaseOffset': r'$\frac{\Delta \phi}{\pi}$',
                  'deltaPspin': r'$\Delta P_\mathrm{spin}$ [s]'
                  }

        fig, ax = self.plot_1D(key, xrescale=rescales_defaults[key],
                               xlabel=labels[key], savefig=False)
        ax.set_title(
            'T={} days, $f$={} Hz, $\log\mathcal{{B}}_{{S/A}}$={:.1f}'
            .format(self.duration/86400, self.F0, Bsa))
        fig.tight_layout()
        fig.savefig('{}/{}_1D.png'.format(self.outdir, self.label))


class DMoff_NO_SPIN(GridSearch):
    """ DMoff test using SSBPREC_NO_SPIN """
    @helper_functions.initializer
    def __init__(self, par, label, outdir, sftfilepattern, minStartTime=None,
                 maxStartTime=None, minCoverFreq=None, maxCoverFreq=None,
                 detectors=None, injectSources=None, assumeSqrtSX=None):
        """
        Parameters
        ----------
        par: dict, str
            Either a par dictionary (containing 'F0', 'F1', 'Alpha', 'Delta'
            and 'tref') or a path to a .par file to read in the F0, F1 etc
        label, outdir: str
            A label and directory to read/write data from/to
        sftfilepattern: str
            Pattern to match SFTs using wildcards (*?) and ranges [0-9];
            mutiple patterns can be given separated by colons.
        minStartTime, maxStartTime: int
            GPS seconds of the start time and end time

        For all other parameters, see `pyfstat.ComputeFStat` for details
        """

        if os.path.isdir(outdir) is False:
            os.mkdir(outdir)

        if type(par) == dict:
            self.par = par
        elif type(par) == str and os.path.isfile(par):
            self.par = read_par(filename=par)
        else:
            raise ValueError('The .par file does not exist')

        self.nsegs = 1
        self.BSGL = False

        self.tref = self.par['tref']
        self.F1s = [self.par.get('F1', 0)]
        self.F2s = [self.par.get('F2', 0)]
        self.Alphas = [self.par['Alpha']]
        self.Deltas = [self.par['Delta']]
        self.Re = 6.371e6
        self.c = 2.998e8
        a0 = self.Re/self.c  # *np.cos(self.par['Delta'])
        self.m0 = np.max([4, int(np.ceil(2*np.pi*self.par['F0']*a0))])
        logging.info(
            'Setting up DMoff_NO_SPIN search with m0 = {}'.format(self.m0))

    def get_results(self):
        """ Compute the three summed detection statistics

        Returns
        -------
            m0, twoF_SUM, twoFstar_SUM_SIDEREAL, twoFstar_SUM_TERRESTRIAL

        """
        self.SSBprec = lalpulsar.SSBPREC_RELATIVISTIC
        self.set_out_file('SSBPREC_RELATIVISTIC')
        self.F0s = [self.par['F0']+j/lal.DAYSID_SI for j in range(-4, 5)]
        self.run()
        twoF_SUM = np.sum(self.data[:, -1])

        self.SSBprec = lalpulsar.SSBPREC_NO_SPIN
        self.set_out_file('SSBPREC_NO_SPIN')
        self.F0s = [self.par['F0']+j/lal.DAYSID_SI
                    for j in range(-self.m0, self.m0+1)]
        self.run()
        twoFstar_SUM = np.sum(self.data[:, -1])

        self.set_out_file('SSBPREC_NO_SPIN_TERRESTRIAL')
        self.F0s = [self.par['F0']+j/lal.DAYJUL_SI
                    for j in range(-self.m0, self.m0+1)]
        self.run()
        twoFstar_SUM_terrestrial = np.sum(self.data[:, -1])

        return self.m0, twoF_SUM, twoFstar_SUM, twoFstar_SUM_terrestrial