How to use exclude_elements method in toolium

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laser_ranging.py

Source:laser_ranging.py

1#!/usr/bin/python32# laser_ranging.py3"""Constraints on the stochastic GW background from laser ranging."""4__author__ = ("Alexander C. Jenkins",)5__contact__ = ("alexander.jenkins@kcl.ac.uk",)6__version__ = "0.1"7__date__ = "2021/07"8import numpy as np9from scipy.optimize import root_scalar10from scipy.stats import chi211from gwresonance import Binary, gamma, sma_from_per, v_rms, AU, NMAX12#-----------------------------------------------------------------------------#13def fisher(x,14           t_obs,15           n_obs,16           sigma=3.e-3,17           m1=3.00345e-06,18           m2=3.69223e-08,19           ):20    """Laser-ranging Fisher matrix for measuring orbital elements.21    Parameters22    ----------23    x : array_like, shape (6,)24        Orbital elements of the binary.25    t_obs : float26        Observation period over which each measurement of the binary27        orbital elements is performed, in seconds.28    n_obs : float29        Mean number of normal point observations recorded per30        observation period.31    sigma : float, optional32        RMS distance noise for each normal point, in metres. Default is33        3mm.34    m1 : float, optional35        Mass of the primary body in solar units. Default is the Earth's36        mass.37    m2 : float, optional38        Mass of the secondary body in solar units. Default is the39        Moon's mass.40    Returns41    -------42    array, shape (6,6)43        Fisher matrix for the orbital elements.44    """45    out = np.zeros((6, 6))46    (per, ecc, inc, asc, arg, eps) = x47    if ecc == None:48        out[0, 0] = 4. / 9. / per**2.49    else:50        g = gamma(ecc)51        out[0, 0] = (4. / 9. / per**2. * (1. + 3.*ecc + 27./16.*ecc**2.52                                          + 4.*ecc**3. + 315./256.*ecc**4.)53                     + 2. / 3. * (np.pi * ecc * t_obs)**2. / per**4.54                     * (1. + 0.25*ecc**2.))55        out[0, 1] = 0.75 / per * ecc * (1. + 8./9.*ecc + 5./8.*ecc**2.56                                        + 8./45.*ecc**3.)57        out[1, 0] = out[0, 1]58        out[1, 1] = 2. - g - (1. - g) / ecc**2.59        out[5, 5] = 1. - g60    return out * n_obs * (sma_from_per(per, m1+m2) * AU / sigma) ** 2.61def likelihood_ratio(sgwb,62                     x_init,63                     times,64                     t_obs,65                     n_obs,66                     sigma=3.e-3,67                     m1=3.00345e-06,68                     m2=3.69223e-08,69                     exclude_elements=None,70                     ):71    """Calculate the likelihood ratio statistic for a binary pulsar.72    Parameters73    ----------74    sgwb : float or function75        SGWB energy density spectrum. If ``sgwb'' is a float, the76        spectrum is assumed to be scale-invariant.77    x_init : array_like, shape (6,)78        Initial orbital elements of the binary.79    times : array_like80        Array of times at which the binary orbital elements are81        measured, in seconds.82    t_obs : float83        Observation period over which each measurement of the binary84        orbital elements is performed, in seconds.85    n_obs : float86        Mean number of normal point observations recorded per87        observation period.88    sigma : float, optional89        RMS distance noise for each normal point, in metres. Default is90        3mm.91    m1 : float, optional92        Mass of the primary body in solar units. Default is the Earth's93        mass.94    m2 : float, optional95        Mass of the secondary body in solar units. Default is the96        Moon's mass.97    exclude_elements : array_like, shape (6,), optional98        Exclude orbital elements from the calculation by setting the99        corresponding elements of this array to ``False'', and the100        rest to ``True''. Default depends on the value of ``low_ecc''.101    Returns102    -------103    float104        Value of the maximum likelihood ratio statistic.105    """106    b = Binary(sgwb,107               x_init,108               m1=m1,109               m2=m2,110               )111    b.evolve(times[-1],112             t_eval=times)113    out = 0.114    if exclude_elements is None:115        exclude_elements = np.array([True]*2 +[False]*2 +[True] +[False])116    ex = exclude_elements117    for t in times:118        x0 = b.x0[b.t == t][0]119        dx = b.dx[b.t == t][0][ex]120        cov = b.cov[b.t == t][0][:,ex][ex,:]121        fish = fisher(x0, t_obs, n_obs, sigma=sigma, m1=m1, m2=m2)[:,ex][ex,:]122        out += np.linalg.multi_dot([dx, fish, dx])123        out += np.dot(fish, cov).trace()124        (s, logdet) = np.linalg.slogdet(np.eye(len(dx)) + np.dot(fish, cov))125        out -= s * logdet126    return out127def power_law_ul(alpha,128                 f_ref,129                 x_init,130                 times,131                 t_obs,132                 n_obs,133                 sigma=3.e-3,134                 m1=3.00345e-06,135                 m2=3.69223e-08,136                 confidence=0.95,137                 exclude_elements=None,138                 bracket=(-20., +20.),139                 ):140    r"""Calculate a pulsar-timing upper limit on a power-law SGWB.141    Outputs a forecast upper limit on :math:`\Omega_\mathrm{ref}`,142    where the SGWB spectrum is given by143    .. math::144        \Omega_\mathrm{gw}(f)145        = \Omega_\mathrm{ref} (f / f_\mathrm{ref})^\alpha.146    Parameters147    ----------148    alpha : float149        SGWB power-law index.150    f_ref : float151        SGWB reference frequency at which the upper limit is computed.152    x_init : array_like, shape (6,) or (N, 6)153        Initial orbital elements of the binary.154    times : array_like155        Array of times at which the binary orbital elements are156        measured, in seconds.157    t_obs : float158        Observation period over which each measurement of the binary159        orbital elements is performed, in seconds.160    n_obs : float161        Mean number of normal point observations recorded per162        observation period.163    sigma : float, optional164        RMS distance noise for each normal point, in metres. Default is165        3mm.166    m1 : float, optional167        Mass of the primary body in solar units. Default is the Earth's168        mass.169    m2 : float, optional170        Mass of the secondary body in solar units. Default is the171        Moon's mass.172    confidence : float, optional173        Set the p-value of the upper limit.174    exclude_elements : array_like, shape (6,), optional175        Exclude orbital elements from the calculation by setting the176        corresponding elements of this array to ``False'', and the177        rest to ``True''.178    bracket : array_like, shape (2,), optional179        Bracket for the root-finding algorithm. The entries should be180        estimated maximum and minimum values of181        :math:`log_{10}\Omega_\mathrm{ref}`.182    Returns183    -------184    float185        Upper limit on :math:`\Omega_\mathrm{ref}`.186    """187    chi2_crit = chi2.ppf(confidence, 1)188    func = (lambda logohm:189            likelihood_ratio(lambda f: 10.**logohm * (f/f_ref)**alpha,190                             x_init, times, t_obs, n_obs, sigma=sigma,191                             m1=m1, m2=m2, exclude_elements=exclude_elements)192            - chi2_crit)193    if func(bracket[1]) < 0.:194        print("Warning: upper limit lies above bracket.")195        return 10. ** bracket[1]196    elif func(bracket[0]) > 0.:197        print("Warning: upper limit lies below bracket.")198        return 10. ** bracket[0]199    else:200        sol = root_scalar(func,201                          method="brentq",202                          bracket=bracket,203                          )204        return 10. ** sol.root205def pi_curve(freqs,206             x_init,207             times,208             t_obs,209             n_obs,210             sigma=3.e-3,211             m1=3.00345e-06,212             m2=3.69223e-08,213             confidence=0.95,214             alphas=None,215             exclude_elements=None,216             bracket=(-20., +20.),217             verbose=False,218             ):219    """Calculate a binary pulsar's SGWB sensitivity curve.220    Returns the power-law integrated (PI) curve, as defined in [1]_.221    Parameters222    ----------223    freqs : array_like of floats224        Frequencies at which the sensitivity should be computed.225    x_init : array_like, shape (6,) or (N, 6)226        Initial orbital elements of the binary.227    times : array_like228        Array of times at which the binary orbital elements are229        measured, in seconds.230    t_obs : float231        Observation period over which each measurement of the binary232        orbital elements is performed, in seconds.233    n_obs : float234        Mean number of normal point observations recorded per235        observation period.236    sigma : float, optional237        RMS distance noise for each normal point, in metres. Default is238        3mm.239    m1 : float, optional240        Mass of the primary body in solar units. Default is the Earth's241        mass.242    m2 : float, optional243        Mass of the secondary body in solar units. Default is the244        Moon's mass.245    confidence : float, optional246        Set the p-value of the upper limit.247    alphas : array_like of floats, optional248        Set of power-law indices which should be used to construct the249        sensitivity curve.250    exclude_elements : array_like, shape (6,), optional251        Exclude orbital elements from the calculation by setting the252        corresponding elements of this array to ``False'', and the253        rest to ``True''.254    bracket : array_like, shape (2,), optional255        Bracket for the root-finding algorithm. The entries should be256        estimated maximum and minimum values of257        :math:`log_{10}\Omega_\mathrm{ref}`.258    verbose : bool, optional259        Control the level of output.260    Returns261    -------262    array of floats263        The value of the sensitivity curve at each of the frequencies264        in ``freqs''.265    References266    ----------267    .. [1] Eric Thrane and Joseph D. Romano, "Sensitivity curves for268        searches for gravitational-wave backgrounds," Phys. Rev. D 88,269        124032 (2013).270    """271    if alphas is None:272        alphas = np.linspace(-10., 10., 81)273    nf = len(freqs)274    na = len(alphas)275    curves = np.zeros((nf, na))276    x_init = np.array(x_init)277    f_ref = 1. / x_init[0]278    if verbose:279        print("Calculating PI curve...")280    for i, alpha in enumerate(alphas):281        if verbose:282            print("alpha = "+str(alpha))283        ul = power_law_ul(alpha, f_ref, x_init, times, t_obs, n_obs,284                          sigma=sigma, m1=m1, m2=m2, confidence=confidence,285                          exclude_elements=exclude_elements, bracket=bracket)286        curves[:, i] = ul * (freqs / f_ref) ** alpha287    return np.max(curves, -1)288def comb_ul(x_init,289            times,290            t_obs,291            n_obs,292            sigma=3.e-3,293            m1=3.00345e-06,294            m2=3.69223e-08,295            confidence=0.95,296            alphas=None,297            exclude_elements=None,298            bracket=(-20., +20.),299            verbose=False,300            ):301    """Calculate a binary pulsar's SGWB sensitivity at each harmonic.302    Returns the SGWB upper limit corresponding to the discrete set of303    frequencies ``[f0, 2*f0, 3*f0, ..., nmax*f0]'', where ``f0'' is the304    base frequency (inverse of the binary period), and ``nmax'' is the305    maximum harmonic (usually 20, but may be less for short periods).306    Parameters307    ----------308    x_init : array_like, shape (6,)309        Initial orbital elements of the binary.310    times : array_like311        Array of times at which the binary orbital elements are312        measured, in seconds.313    t_obs : float314        Observation period over which each measurement of the binary315        orbital elements is performed, in seconds.316    n_obs : float317        Mean number of normal point observations recorded per318        observation period.319    sigma : float, optional320        RMS distance noise for each normal point, in metres. Default is321        3mm.322    m1 : float, optional323        Mass of the primary body in solar units. Default is the Earth's324        mass.325    m2 : float, optional326        Mass of the secondary body in solar units. Default is the327        Moon's mass.328    confidence : float, optional329        Set the p-value of the upper limit.330    alphas : array_like of floats, optional331        Set of power-law indices which should be used to construct the332        sensitivity curve.333    exclude_elements : array_like, shape (6,), optional334        Exclude orbital elements from the calculation by setting the335        corresponding elements of this array to ``False'', and the336        rest to ``True''.337    bracket : array_like, shape (2,), optional338        Bracket for the root-finding algorithm. The entries should be339        estimated maximum and minimum values of340        :math:`log_{10}\Omega_\mathrm{ref}`.341    verbose : bool, optional342        Control the level of output.343    Returns344    -------345    array of floats346        The SGWB upper limit at the first few of the binary's harmonic347        frequencies.348    """349    per = x_init[0]350    f0 = 1. / per351    nmax = min(int(np.floor(v_rms(per, m1+m2) ** -1.)), NMAX)352    chi2_crit = chi2.ppf(confidence, 1)353    comb = []354    if verbose:355        print("Calculating comb...")356    for n in range(1, nmax+1):357        if verbose:358            print("Harmonic {} of {}".format(n, nmax))359        func = (lambda logohm:360            likelihood_ratio(lambda f: 10.**logohm361                             * np.heaviside(0.1*f0 - abs(f-n*f0), 0.),362                             x_init, times, t_obs, n_obs, sigma=sigma,363                             m1=m1, m2=m2, exclude_elements=exclude_elements)364            - chi2_crit)365        if func(bracket[1]) < 0.:366            print("Warning: upper limit lies above bracket.")367            comb.append(10. ** bracket[1])368        elif func(bracket[0]) > 0.:369            print("Warning: upper limit lies below bracket.")370            comb.append(10. ** bracket[0])371        else:372            sol = root_scalar(func,373                              method="brentq",374                              bracket=bracket,375                              )376            comb.append(10. ** sol.root)377    return np.array(comb)...

config.py

Source:config.py

1from common.configuration_loader import *2from logic_actions import logic_actions_camera3from logic_actions import logic_actions_dns4from logic_actions import logic_actions_elk5from logic_actions import logic_actions_filebeat6from logic_actions import logic_actions_ldap7from logic_actions import logic_actions_mail8from logic_actions import logic_actions_proxy9from logic_actions import logic_actions_rsyslog10from logic_actions import logic_actions_samba11from logic_actions import logic_actions_security12from logic_actions import logic_actions_vpn13from logic_actions import logic_actions_web14from logic_actions import logic_actions_utils15import os16current_path = os.path.dirname(os.path.abspath(__file__))17# Software version18version_file = os.path.join(current_path, "..", "version.ini")19# Workstations functions20workstations_file = os.path.join(current_path, "workstations", "common.ini")21exclude_elements = ["Fore", "Style", "__builtins__", "__cached__", "__doc__", "__file__", "__loader__", "__name__",22                    "__package__", "__spec__", "Optional", "time", "os", "cv2", "time", "json", "random", "hashlib",23                    "subprocess", "crypto"]24class Config:25    @staticmethod26    def get_version():27        return parse_value(version_file, "SI_simulator", "version")28    @staticmethod29    def get_camera_methods():30        return [f for f in dir(logic_actions_camera) if f not in exclude_elements]31    @staticmethod32    def get_dns_methods():33        return [f for f in dir(logic_actions_dns) if f not in exclude_elements]34    @staticmethod35    def get_elk_methods():36        return [f for f in dir(logic_actions_elk) if f not in exclude_elements]37    @staticmethod38    def get_filebeat_methods():39        return [f for f in dir(logic_actions_filebeat) if f not in exclude_elements]40    @staticmethod41    def get_ldap_methods():42        return [f for f in dir(logic_actions_ldap) if f not in exclude_elements]43    @staticmethod44    def get_mail_methods():45        return [f for f in dir(logic_actions_mail) if f not in exclude_elements]46    @staticmethod47    def get_proxy_methods():48        return [f for f in dir(logic_actions_proxy) if f not in exclude_elements]49    @staticmethod50    def get_rsyslog_methods():51        return [f for f in dir(logic_actions_rsyslog) if f not in exclude_elements]52    @staticmethod53    def get_samba_methods():54        return [f for f in dir(logic_actions_samba) if f not in exclude_elements]55    @staticmethod56    def get_security_methods():57        return [f for f in dir(logic_actions_security) if f not in exclude_elements]58    @staticmethod59    def get_utils_methods():60        return [f for f in dir(logic_actions_utils) if f not in exclude_elements]61    @staticmethod62    def get_vpn_methods():63        return [f for f in dir(logic_actions_vpn) if f not in exclude_elements]64    @staticmethod65    def get_web_methods():66        return [f for f in dir(logic_actions_web) if f not in exclude_elements]67    @staticmethod68    def get_workstations_methods():69        return parse_values_list(workstations_file, "FUNCTIONS", "common")70    @staticmethod71    def get_available_workstations():72        return parse_values_list(workstations_file, "SIMULATION", "workstations")73    @staticmethod74    def get_authorized_values(arg):75        values = []76        if arg in authorized_args.keys():77            values = authorized_args[arg]78        return values79def compare_d_lists(first_list, second_list):80    # Arguments are lists of dictionaries81    for base in first_list:82        for compared in second_list:83            if base["name"] == compared["name"]:84                base.update(compared)85                continue86    return first_list87# Switch88workstation_methods = {89    "camera": Config.get_camera_methods,90    "dns": Config.get_dns_methods,91    "elk": Config.get_elk_methods,92    "filebeat": Config.get_filebeat_methods,  # TODO :add filebeat methods to common93    "ldap": Config.get_ldap_methods,94    "mail": Config.get_mail_methods,95    "proxy": Config.get_proxy_methods,96    "router": Config.get_workstations_methods,97    "rsyslog": Config.get_rsyslog_methods,98    "samba": Config.get_samba_methods,99    "security": Config.get_security_methods,100    "utils": Config.get_utils_methods,101    "vpn": Config.get_vpn_methods,102    "web": Config.get_web_methods,103    "workstation": Config.get_workstations_methods104}105authorized_args = {106    "install": ["module"],107    "execute_command": ["command", "execute_exit_code"],108    "add_nameserver": ["nameserver_ip"],109    "rsyslog_client": ["ip_log_server", "log_files"],110    "install_gnu_social_network": ["server_ip", "domain_name"],111    "download_file": [],112    "generate_root_ca": ["private_key_ca_certificate_name", "bits", "version", "serial", "C", "ST", "L", "O", "CN", "days_validity"],113    "generate_middle_certifications": ["ca_holder", "ca_name", "private_key_middle_certificate_name", "bits", "version", "serial", "C", "ST", "L", "O", "CN", "days_validity"],114    "generate_certificates": ["ca_holder", "ca_name", "middle_holder", "middle_name", "private_key_certificate_name", "bits", "version", "serial", "C", "ST", "L", "O", "CN", "days_validity", "dns"],115    "dns_installation": ["domain_name", "ip_resolution"],116    "dns_resolve_name": ["domain_name", "ip_resolution", "mail", "alias"],117    "ldap_create_domaine": ["root_password", "domaine_name", "domain", "organization", "ip_log_server"],118    "ldap_add_user": ["hostname", "username", "objectClass", "mail", "sn", "dn", "domain", "homeDirectory", "loginShell",119                      "password", "uidNumber", "gidNumber"],120    "ldap_client_config": ["ldap_ip", "base", "uri", "ldap_admin"],121    "mail_installation": ["ldap_ip", "ldap_domain", "ldap_dn", "ldap_manager", "ldap_manager_password", "ldap_port", "domain_name", "users_mailbox"],122    "enable_ssl": ["cert_path", "key_path", "ca_dir", "cas_path"],123    "enable_ssl_imapd": ["cert_path", "key_path", "ca_dir", "cas_path"],124    "enable_ssl_postfix": ["cert_path", "key_path", "ca_dir", "cas_path"],125    "create_local_user": ["username", "password"],126    "configure_iptables": ["share_file_name", "comment", "private", "browseable", "writable", "valid_users", "users"],127    "install_samba": [],128    "add_share_file": [],129    "install_virtual_camera": ["video_url", "remote_video_path_file"],130    "install_motion": ["motion_port", "security"],131    "install_zoneminder": [],132    "install_elk": ["logstash", "elasticsearch", "kibana", "fqdn_host", "ip_fqdn", "admin_name", "admin_passwd"],133    "push_sim_user": [],...

schema.py

Source:schema.py

1from marshmallow import fields, post_load, pre_dump2from marshmallow_sqlalchemy import SQLAlchemySchema3from api.models import Configurations4class GetConfigSchema(SQLAlchemySchema):5    ip = fields.IP(required=True)6    name = fields.Str(required=True)7class CreateConfigSchema(SQLAlchemySchema):8    class Meta:9        model = Configurations10        load_instance = True11    ip = fields.Str(required=True)12    name = fields.Str(required=True)13    block_iso = fields.Bool(required=True)14    exclude_elements = fields.List(fields.Str, required=True)15    @pre_dump16    def pre_dump(self, data, **kwargs):17        if data is not None and data.exclude_elements:18            data.exclude_elements = [19                element for element in data.exclude_elements.split(",")20            ]21            return data22    @post_load23    def post_load(self, data, **kwargs):24        if data is not None and data.exclude_elements:25            data.exclude_elements = ",".join(data.exclude_elements)...

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