Exemple #1
0
    def initialize(self, key):
        super().initialize(key)

        # for now, just use white noise
        self.data_mat = self.sigma_mat.copy()
        self.data_mat_last = self.data_mat.copy()

        #Set up p0 and the independent sampler
        fname = Starfish.specfmt.format(self.spectrum_id,
                                        self.order) + "phi.json"
        phi = PhiParam.load(fname)
        self.p0 = phi.cheb
        cov = np.diag(Starfish.config["cheb_jump"]**2 * np.ones(len(self.p0)))

        def lnfunc(p):
            # turn this into pars
            self.update_Phi(p)
            lnp = self.evaluate()
            self.logger.debug("Evaluated Phi parameters: {} {}".format(p, lnp))
            return lnp

        def rejectfn():
            self.logger.debug("Calling Phi revertfn.")
            self.revert_Phi()

        self.sampler = StateSampler(lnfunc,
                                    self.p0,
                                    cov,
                                    query_lnprob=self.get_lnprob,
                                    rejectfn=rejectfn,
                                    debug=True)
Exemple #2
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    def initialize(self, key):
        # Run through the standard initialization
        super().initialize(key)

        # for now, start with white noise
        self.data_mat = self.sigma_mat.copy()
        self.data_mat_last = self.data_mat.copy()

        #Set up p0 and the independent sampler
        fname = Starfish.specfmt.format(self.spectrum_id, self.order) + "phi.json"
        phi = PhiParam.load(fname)

        # Set the regions to None, since we don't want to include them even if they
        # are there
        phi.regions = None

        #Loading file that was previously output
        # Convert PhiParam object to an array
        self.p0 = phi.toarray()

        jump = Starfish.config["Phi_jump"]
        cheb_len = (self.npoly - 1) if self.chebyshevSpectrum.fix_c0 else self.npoly
        cov_arr = np.concatenate((Starfish.config["cheb_jump"]**2 * np.ones((cheb_len,)), np.array([jump["sigAmp"], jump["logAmp"], jump["l"]])**2 ))
        cov = np.diag(cov_arr)

        def lnfunc(p):
            # Convert p array into a PhiParam object
            ind = self.npoly
            if self.chebyshevSpectrum.fix_c0:
                ind -= 1

            cheb = p[0:ind]
            sigAmp = p[ind]
            ind+=1
            logAmp = p[ind]
            ind+=1
            l = p[ind]

            par = PhiParam(self.spectrum_id, self.order, self.chebyshevSpectrum.fix_c0, cheb, sigAmp, logAmp, l)

            self.update_Phi(par)

            # sigAmp must be positive (this is effectively a prior)
            # See https://github.com/iancze/Starfish/issues/26
            if not (0.0 < sigAmp): 
                self.lnprob_last = self.lnprob
                lnp = -np.inf
                self.logger.debug("sigAmp was negative, returning -np.inf")
                self.lnprob = lnp # Same behavior as self.evaluate()
            else:
                lnp = self.evaluate()
                self.logger.debug("Evaluated Phi parameters: {} {}".format(par, lnp))

            return lnp

        def rejectfn():
            self.logger.debug("Calling Phi revertfn.")
            self.revert_Phi()

        self.sampler = StateSampler(lnfunc, self.p0, cov, query_lnprob=self.get_lnprob, rejectfn=rejectfn, debug=True)
Exemple #3
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    def initialize(self, key):
        # Run through the standard initialization
        super().initialize(key)

        # for now, start with white noise
        self.data_mat = self.sigma_mat.copy()
        self.data_mat_last = self.data_mat.copy()

        #Set up p0 and the independent sampler
        fname = Starfish.specfmt.format(self.spectrum_id, self.order) + "phi.json"
        phi = PhiParam.load(fname)

        # Set the regions to None, since we don't want to include them even if they
        # are there
        phi.regions = None

        #Loading file that was previously output
        # Convert PhiParam object to an array
        self.p0 = phi.toarray()

        jump = Starfish.config["Phi_jump"]
        cheb_len = (self.npoly - 1) if self.chebyshevSpectrum.fix_c0 else self.npoly
        cov_arr = np.concatenate((Starfish.config["cheb_jump"]**2 * np.ones((cheb_len,)), np.array([jump["sigAmp"], jump["logAmp"], jump["l"]])**2 ))
        cov = np.diag(cov_arr)

        def lnfunc(p):
            # Convert p array into a PhiParam object
            ind = self.npoly
            if self.chebyshevSpectrum.fix_c0:
                ind -= 1

            cheb = p[0:ind]
            sigAmp = p[ind]
            ind+=1
            logAmp = p[ind]
            ind+=1
            l = p[ind]

            par = PhiParam(self.spectrum_id, self.order, self.chebyshevSpectrum.fix_c0, cheb, sigAmp, logAmp, l)

            self.update_Phi(par)

            # sigAmp must be positive (this is effectively a prior)
            # See https://github.com/iancze/Starfish/issues/26
            if not (0.0 < sigAmp): 
                self.lnprob_last = self.lnprob
                lnp = -np.inf
                self.logger.debug("sigAmp was negative, returning -np.inf")
                self.lnprob = lnp # Same behavior as self.evaluate()
            else:
                lnp = self.evaluate()
                self.logger.debug("Evaluated Phi parameters: {} {}".format(par, lnp))

            return lnp

        def rejectfn():
            self.logger.debug("Calling Phi revertfn.")
            self.revert_Phi()

        self.sampler = StateSampler(lnfunc, self.p0, cov, query_lnprob=self.get_lnprob, rejectfn=rejectfn, debug=True)
Exemple #4
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    def initialize(self, key):
        super().initialize(key)

        # for now, just use white noise
        self.data_mat = self.sigma_mat.copy()
        self.data_mat_last = self.data_mat.copy()

        #Set up p0 and the independent sampler
        fname = Starfish.specfmt.format(self.spectrum_id, self.order) + "phi.json"
        phi = PhiParam.load(fname)
        self.p0 = phi.cheb
        cov = np.diag(Starfish.config["cheb_jump"]**2 * np.ones(len(self.p0)))

        def lnfunc(p):
            # turn this into pars
            self.update_Phi(p)
            lnp = self.evaluate()
            self.logger.debug("Evaluated Phi parameters: {} {}".format(p, lnp))
            return lnp

        def rejectfn():
            self.logger.debug("Calling Phi revertfn.")
            self.revert_Phi()

        self.sampler = StateSampler(lnfunc, self.p0, cov, query_lnprob=self.get_lnprob, rejectfn=rejectfn, debug=True)
Exemple #5
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    def initialize(self, key):
        # Run through the standard initialization
        super().initialize(key)

        # for now, start with white noise
        self.data_mat = self.sigma_mat.copy()
        self.data_mat_last = self.data_mat.copy()

        #Set up p0 and the independent sampler
        fname = Starfish.specfmt.format(self.spectrum_id, self.order) + "phi.json"
        phi = PhiParam.load(fname)

        # print("Phi.regions", phi.regions)
        # import sys
        # sys.exit()
        # Get the regions matrix
        region_func = make_k_func_region(phi)

        max_r = 4.0 * np.max(phi.regions, axis=0)[2]

        self.region_mat = get_dense_C(self.wl, k_func=region_func, max_r=max_r)

        print(self.region_mat)

        # Then set phi to None
        phi.regions = None

        #Loading file that was previously output
        # Convert PhiParam object to an array
        self.p0 = phi.toarray()

        jump = Starfish.config["Phi_jump"]
        cheb_len = (self.npoly - 1) if self.chebyshevSpectrum.fix_c0 else self.npoly
        cov_arr = np.concatenate((Starfish.config["cheb_jump"]**2 * np.ones((cheb_len,)), np.array([jump["sigAmp"], jump["logAmp"], jump["l"]])**2 ))
        cov = np.diag(cov_arr)

        def lnfunc(p):
            # Convert p array into a PhiParam object
            ind = self.npoly
            if self.chebyshevSpectrum.fix_c0:
                ind -= 1

            cheb = p[0:ind]
            sigAmp = p[ind]
            ind+=1
            logAmp = p[ind]
            ind+=1
            l = p[ind]

            phi = PhiParam(self.spectrum_id, self.order, self.chebyshevSpectrum.fix_c0, cheb, sigAmp, logAmp, l)

            self.update_Phi(phi)
            lnp = self.evaluate()
            self.logger.debug("Evaluated Phi parameters: {} {}".format(phi, lnp))
            return lnp

        def rejectfn():
            self.logger.debug("Calling Phi revertfn.")
            self.revert_Phi()

        self.sampler = StateSampler(lnfunc, self.p0, cov, query_lnprob=self.get_lnprob, rejectfn=rejectfn, debug=True)
Exemple #6
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class SampleThetaPhiLines(Order):

    def initialize(self, key):
        # Run through the standard initialization
        super().initialize(key)

        # for now, start with white noise
        self.data_mat = self.sigma_mat.copy()
        self.data_mat_last = self.data_mat.copy()

        #Set up p0 and the independent sampler
        fname = Starfish.specfmt.format(self.spectrum_id, self.order) + "phi.json"
        phi = PhiParam.load(fname)

        # print("Phi.regions", phi.regions)
        # import sys
        # sys.exit()
        # Get the regions matrix
        region_func = make_k_func_region(phi)

        max_r = 4.0 * np.max(phi.regions, axis=0)[2]

        self.region_mat = get_dense_C(self.wl, k_func=region_func, max_r=max_r)

        print(self.region_mat)

        # Then set phi to None
        phi.regions = None

        #Loading file that was previously output
        # Convert PhiParam object to an array
        self.p0 = phi.toarray()

        jump = Starfish.config["Phi_jump"]
        cheb_len = (self.npoly - 1) if self.chebyshevSpectrum.fix_c0 else self.npoly
        cov_arr = np.concatenate((Starfish.config["cheb_jump"]**2 * np.ones((cheb_len,)), np.array([jump["sigAmp"], jump["logAmp"], jump["l"]])**2 ))
        cov = np.diag(cov_arr)

        def lnfunc(p):
            # Convert p array into a PhiParam object
            ind = self.npoly
            if self.chebyshevSpectrum.fix_c0:
                ind -= 1

            cheb = p[0:ind]
            sigAmp = p[ind]
            ind+=1
            logAmp = p[ind]
            ind+=1
            l = p[ind]

            phi = PhiParam(self.spectrum_id, self.order, self.chebyshevSpectrum.fix_c0, cheb, sigAmp, logAmp, l)

            self.update_Phi(phi)
            lnp = self.evaluate()
            self.logger.debug("Evaluated Phi parameters: {} {}".format(phi, lnp))
            return lnp

        def rejectfn():
            self.logger.debug("Calling Phi revertfn.")
            self.revert_Phi()

        self.sampler = StateSampler(lnfunc, self.p0, cov, query_lnprob=self.get_lnprob, rejectfn=rejectfn, debug=True)

    def update_Phi(self, phi):
        self.logger.debug("Updating nuisance parameters to {}".format(phi))

        # Read off the Chebyshev parameters and update
        self.chebyshevSpectrum.update(phi.cheb)

        # Check to make sure the global covariance parameters make sense
        if phi.sigAmp < 0.1:
            raise C.ModelError("sigAmp shouldn't be lower than 0.1, something is wrong.")

        max_r = 6.0 * phi.l # [km/s]

        # Create a partial function which returns the proper element.
        k_func = make_k_func(phi)

        # Store the previous data matrix in case we want to revert later
        self.data_mat_last = self.data_mat
        self.data_mat = get_dense_C(self.wl, k_func=k_func, max_r=max_r) + phi.sigAmp*self.sigma_mat + self.region_mat

    def finish(self, *args):
        super().finish(*args)
        fname = Starfish.routdir + Starfish.specfmt.format(self.spectrum_id, self.order) + "/mc.hdf5"
        self.sampler.write(fname=fname)
Exemple #7
0
class SampleThetaPhi(Order):

    def initialize(self, key):
        # Run through the standard initialization
        super().initialize(key)

        # for now, start with white noise
        self.data_mat = self.sigma_mat.copy()
        self.data_mat_last = self.data_mat.copy()

        #Set up p0 and the independent sampler
        fname = Starfish.specfmt.format(self.spectrum_id, self.order) + "phi.json"
        phi = PhiParam.load(fname)

        # Set the regions to None, since we don't want to include them even if they
        # are there
        phi.regions = None

        #Loading file that was previously output
        # Convert PhiParam object to an array
        self.p0 = phi.toarray()

        jump = Starfish.config["Phi_jump"]
        cheb_len = (self.npoly - 1) if self.chebyshevSpectrum.fix_c0 else self.npoly
        cov_arr = np.concatenate((Starfish.config["cheb_jump"]**2 * np.ones((cheb_len,)), np.array([jump["sigAmp"], jump["logAmp"], jump["l"]])**2 ))
        cov = np.diag(cov_arr)

        def lnfunc(p):
            # Convert p array into a PhiParam object
            ind = self.npoly
            if self.chebyshevSpectrum.fix_c0:
                ind -= 1

            cheb = p[0:ind]
            sigAmp = p[ind]
            ind+=1
            logAmp = p[ind]
            ind+=1
            l = p[ind]

            par = PhiParam(self.spectrum_id, self.order, self.chebyshevSpectrum.fix_c0, cheb, sigAmp, logAmp, l)

            self.update_Phi(par)

            # sigAmp must be positive (this is effectively a prior)
            # See https://github.com/iancze/Starfish/issues/26
            if not (0.0 < sigAmp): 
                self.lnprob_last = self.lnprob
                lnp = -np.inf
                self.logger.debug("sigAmp was negative, returning -np.inf")
                self.lnprob = lnp # Same behavior as self.evaluate()
            else:
                lnp = self.evaluate()
                self.logger.debug("Evaluated Phi parameters: {} {}".format(par, lnp))

            return lnp

        def rejectfn():
            self.logger.debug("Calling Phi revertfn.")
            self.revert_Phi()

        self.sampler = StateSampler(lnfunc, self.p0, cov, query_lnprob=self.get_lnprob, rejectfn=rejectfn, debug=True)

    def update_Phi(self, p):
        self.logger.debug("Updating nuisance parameters to {}".format(p))

        # Read off the Chebyshev parameters and update
        self.chebyshevSpectrum.update(p.cheb)

        # Check to make sure the global covariance parameters make sense
        #if p.sigAmp < 0.1:
        #   raise C.ModelError("sigAmp shouldn't be lower than 0.1, something is wrong.")

        max_r = 6.0 * p.l # [km/s]

        # Create a partial function which returns the proper element.
        k_func = make_k_func(p)

        # Store the previous data matrix in case we want to revert later
        self.data_mat_last = self.data_mat
        self.data_mat = get_dense_C(self.wl, k_func=k_func, max_r=max_r) + p.sigAmp*self.sigma_mat

    def finish(self, *args):
        super().finish(*args)
        fname = Starfish.routdir + Starfish.specfmt.format(self.spectrum_id, self.order) + "/mc.hdf5"
        self.sampler.write(fname=fname)
Exemple #8
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    jump = Starfish.config["Theta_jump"]
    cov = np.diag(
        np.array(jump["grid"] +
                 [jump["vz"], jump["vsini"], jump["logOmega"]])**2)

    if args.use_cov:
        try:
            cov = np.load('opt_jump.npy')
            print("Found a local optimal jump matrix.")
        except FileNotFoundError:
            print("No optimal jump matrix found, using diagonal jump matrix.")

    sampler = StateSampler(lnprob,
                           p0,
                           cov,
                           query_lnprob=query_lnprob,
                           acceptfn=acceptfn,
                           rejectfn=rejectfn,
                           debug=True,
                           outdir=Starfish.routdir)

    p, lnprob, state = sampler.run_mcmc(p0,
                                        N=args.samples,
                                        incremental_save=args.incremental_save)
    print("Final", p)

    sampler.write()

    # Kill all of the orders
    for pconn in pconns.values():
        pconn.send(("FINISH", None))
        pconn.send(("DIE", None))
Exemple #9
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    def initialize(self, key):
        # Run through the standard initialization
        super().initialize(key)

        # for now, start with white noise
        self.data_mat = self.sigma_mat.copy()
        self.data_mat_last = self.data_mat.copy()

        #Set up p0 and the independent sampler
        fname = Starfish.specfmt.format(self.spectrum_id,
                                        self.order) + "phi.json"
        phi = PhiParam.load(fname)

        # print("Phi.regions", phi.regions)
        # import sys
        # sys.exit()
        # Get the regions matrix
        region_func = make_k_func_region(phi)

        max_r = 4.0 * np.max(phi.regions, axis=0)[2]

        self.region_mat = get_dense_C(self.wl, k_func=region_func, max_r=max_r)

        print(self.region_mat)

        # Then set phi to None
        phi.regions = None

        #Loading file that was previously output
        # Convert PhiParam object to an array
        self.p0 = phi.toarray()

        jump = Starfish.config["Phi_jump"]
        cheb_len = (self.npoly -
                    1) if self.chebyshevSpectrum.fix_c0 else self.npoly
        cov_arr = np.concatenate(
            (Starfish.config["cheb_jump"]**2 * np.ones((cheb_len, )),
             np.array([jump["sigAmp"], jump["logAmp"], jump["l"]])**2))
        cov = np.diag(cov_arr)

        def lnfunc(p):
            # Convert p array into a PhiParam object
            ind = self.npoly
            if self.chebyshevSpectrum.fix_c0:
                ind -= 1

            cheb = p[0:ind]
            sigAmp = p[ind]
            ind += 1
            logAmp = p[ind]
            ind += 1
            l = p[ind]

            phi = PhiParam(self.spectrum_id, self.order,
                           self.chebyshevSpectrum.fix_c0, cheb, sigAmp, logAmp,
                           l)

            self.update_Phi(phi)
            lnp = self.evaluate()
            self.logger.debug("Evaluated Phi parameters: {} {}".format(
                phi, lnp))
            return lnp

        def rejectfn():
            self.logger.debug("Calling Phi revertfn.")
            self.revert_Phi()

        self.sampler = StateSampler(lnfunc,
                                    self.p0,
                                    cov,
                                    query_lnprob=self.get_lnprob,
                                    rejectfn=rejectfn,
                                    debug=True)
Exemple #10
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class SampleThetaPhiLines(Order):
    def initialize(self, key):
        # Run through the standard initialization
        super().initialize(key)

        # for now, start with white noise
        self.data_mat = self.sigma_mat.copy()
        self.data_mat_last = self.data_mat.copy()

        #Set up p0 and the independent sampler
        fname = Starfish.specfmt.format(self.spectrum_id,
                                        self.order) + "phi.json"
        phi = PhiParam.load(fname)

        # print("Phi.regions", phi.regions)
        # import sys
        # sys.exit()
        # Get the regions matrix
        region_func = make_k_func_region(phi)

        max_r = 4.0 * np.max(phi.regions, axis=0)[2]

        self.region_mat = get_dense_C(self.wl, k_func=region_func, max_r=max_r)

        print(self.region_mat)

        # Then set phi to None
        phi.regions = None

        #Loading file that was previously output
        # Convert PhiParam object to an array
        self.p0 = phi.toarray()

        jump = Starfish.config["Phi_jump"]
        cheb_len = (self.npoly -
                    1) if self.chebyshevSpectrum.fix_c0 else self.npoly
        cov_arr = np.concatenate(
            (Starfish.config["cheb_jump"]**2 * np.ones((cheb_len, )),
             np.array([jump["sigAmp"], jump["logAmp"], jump["l"]])**2))
        cov = np.diag(cov_arr)

        def lnfunc(p):
            # Convert p array into a PhiParam object
            ind = self.npoly
            if self.chebyshevSpectrum.fix_c0:
                ind -= 1

            cheb = p[0:ind]
            sigAmp = p[ind]
            ind += 1
            logAmp = p[ind]
            ind += 1
            l = p[ind]

            phi = PhiParam(self.spectrum_id, self.order,
                           self.chebyshevSpectrum.fix_c0, cheb, sigAmp, logAmp,
                           l)

            self.update_Phi(phi)
            lnp = self.evaluate()
            self.logger.debug("Evaluated Phi parameters: {} {}".format(
                phi, lnp))
            return lnp

        def rejectfn():
            self.logger.debug("Calling Phi revertfn.")
            self.revert_Phi()

        self.sampler = StateSampler(lnfunc,
                                    self.p0,
                                    cov,
                                    query_lnprob=self.get_lnprob,
                                    rejectfn=rejectfn,
                                    debug=True)

    def update_Phi(self, phi):
        self.logger.debug("Updating nuisance parameters to {}".format(phi))

        # Read off the Chebyshev parameters and update
        self.chebyshevSpectrum.update(phi.cheb)

        # Check to make sure the global covariance parameters make sense
        if phi.sigAmp < 0.1:
            raise C.ModelError(
                "sigAmp shouldn't be lower than 0.1, something is wrong.")

        max_r = 6.0 * phi.l  # [km/s]

        # Create a partial function which returns the proper element.
        k_func = make_k_func(phi)

        # Store the previous data matrix in case we want to revert later
        self.data_mat_last = self.data_mat
        self.data_mat = get_dense_C(
            self.wl, k_func=k_func,
            max_r=max_r) + phi.sigAmp * self.sigma_mat + self.region_mat

    def finish(self, *args):
        super().finish(*args)
        fname = Starfish.routdir + Starfish.specfmt.format(
            self.spectrum_id, self.order) + "/mc.hdf5"
        self.sampler.write(fname=fname)
Exemple #11
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            pconn.send(("DECIDE", True))

    def rejectfn():
        print("Calling rejectfn")
        for ((spectrum_id, order_id), pconn) in pconns.items():
            pconn.send(("DECIDE", False))

    from Starfish.samplers import StateSampler

    start = Starfish.config["Theta"]
    p0 = np.array(start["grid"] + [start["vz"], start["vsini"], start["logOmega"]])

    jump = Starfish.config["Theta_jump"]
    cov = np.diag(np.array(jump["grid"] + [jump["vz"], jump["vsini"], jump["logOmega"]])**2)

    sampler = StateSampler(lnprob, p0, cov, query_lnprob=query_lnprob, acceptfn=acceptfn, rejectfn=rejectfn, debug=True, outdir=Starfish.routdir)

    p, lnprob, state = sampler.run_mcmc(p0, N=args.samples)
    print("Final", p)

    sampler.write()

    # Kill all of the orders
    for pconn in pconns.values():
        pconn.send(("FINISH", None))
        pconn.send(("DIE", None))

    # Join on everything and terminate
    for p in ps.values():
        p.join()
        p.terminate()
Exemple #12
0
class SampleThetaPhi(Order):

    def initialize(self, key):
        # Run through the standard initialization
        super().initialize(key)

        # for now, start with white noise
        self.data_mat = self.sigma_mat.copy()
        self.data_mat_last = self.data_mat.copy()

        #Set up p0 and the independent sampler
        fname = Starfish.specfmt.format(self.spectrum_id, self.order) + "phi.json"
        phi = PhiParam.load(fname)

        # Set the regions to None, since we don't want to include them even if they
        # are there
        phi.regions = None

        #Loading file that was previously output
        # Convert PhiParam object to an array
        self.p0 = phi.toarray()

        jump = Starfish.config["Phi_jump"]
        cheb_len = (self.npoly - 1) if self.chebyshevSpectrum.fix_c0 else self.npoly
        cov_arr = np.concatenate((Starfish.config["cheb_jump"]**2 * np.ones((cheb_len,)), np.array([jump["sigAmp"], jump["logAmp"], jump["l"]])**2 ))
        cov = np.diag(cov_arr)

        def lnfunc(p):
            # Convert p array into a PhiParam object
            ind = self.npoly
            if self.chebyshevSpectrum.fix_c0:
                ind -= 1

            cheb = p[0:ind]
            sigAmp = p[ind]
            ind+=1
            logAmp = p[ind]
            ind+=1
            l = p[ind]

            par = PhiParam(self.spectrum_id, self.order, self.chebyshevSpectrum.fix_c0, cheb, sigAmp, logAmp, l)

            self.update_Phi(par)

            # sigAmp must be positive (this is effectively a prior)
            # See https://github.com/iancze/Starfish/issues/26
            if not (0.0 < sigAmp): 
                self.lnprob_last = self.lnprob
                lnp = -np.inf
                self.logger.debug("sigAmp was negative, returning -np.inf")
                self.lnprob = lnp # Same behavior as self.evaluate()
            else:
                lnp = self.evaluate()
                self.logger.debug("Evaluated Phi parameters: {} {}".format(par, lnp))

            return lnp

        def rejectfn():
            self.logger.debug("Calling Phi revertfn.")
            self.revert_Phi()

        self.sampler = StateSampler(lnfunc, self.p0, cov, query_lnprob=self.get_lnprob, rejectfn=rejectfn, debug=True)

    def update_Phi(self, p):
        self.logger.debug("Updating nuisance parameters to {}".format(p))

        # Read off the Chebyshev parameters and update
        self.chebyshevSpectrum.update(p.cheb)

        # Check to make sure the global covariance parameters make sense
        #if p.sigAmp < 0.1:
        #   raise C.ModelError("sigAmp shouldn't be lower than 0.1, something is wrong.")

        max_r = 6.0 * p.l # [km/s]

        # Create a partial function which returns the proper element.
        k_func = make_k_func(p)

        # Store the previous data matrix in case we want to revert later
        self.data_mat_last = self.data_mat
        self.data_mat = get_dense_C(self.wl, k_func=k_func, max_r=max_r) + p.sigAmp*self.sigma_mat

    def finish(self, *args):
        super().finish(*args)
        fname = Starfish.routdir + Starfish.specfmt.format(self.spectrum_id, self.order) + "/mc.hdf5"
        self.sampler.write(fname=fname)
Exemple #13
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    from Starfish.samplers import StateSampler

    start = Starfish.config["Theta"]
    p0 = np.array(start["grid"] + [start["vz"], start["vsini"], start["logOmega"]])

    jump = Starfish.config["Theta_jump"]
    cov = np.diag(np.array(jump["grid"] + [jump["vz"], jump["vsini"], jump["logOmega"]])**2)

    if args.use_cov:
        try:
            cov = np.load('opt_jump.npy')
            print("Found a local optimal jump matrix.")
        except FileNotFoundError:
            print("No optimal jump matrix found, using diagonal jump matrix.")

    sampler = StateSampler(lnprob, p0, cov, query_lnprob=query_lnprob, acceptfn=acceptfn, rejectfn=rejectfn, debug=True, outdir=Starfish.routdir)

    p, lnprob, state = sampler.run_mcmc(p0, N=args.samples, incremental_save=args.incremental_save)
    print("Final", p)

    sampler.write()

    # Kill all of the orders
    for pconn in pconns.values():
        pconn.send(("FINISH", None))
        pconn.send(("DIE", None))

    # Join on everything and terminate
    for p in ps.values():
        p.join()
        p.terminate()