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How to use exclude_elements method in toolium
Best Python code snippet using toolium_python
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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