redback 1.0.1__tar.gz → 1.0.3__tar.gz

{redback-1.0.1 → redback-1.0.3}/PKG-INFO

@@ -1,17 +1,54 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: redback
-Version: 1.0.1
+Version: 1.0.3
 Summary: A Bayesian inference pipeline for electromagnetic transients
 Home-page: https://github.com/nikhil-sarin/redback
 Author: Nikhil Sarin, Moritz Huebner
-Author-email: nikhil.sarin@su.se
+Author-email: nsarin.astro@gmail.com
 License: GNU General Public License v3 (GPLv3)
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.7
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENCE.md
+Requires-Dist: numpy==1.26.0
+Requires-Dist: setuptools
+Requires-Dist: pandas
+Requires-Dist: scipy<1.14.0
+Requires-Dist: selenium
+Requires-Dist: matplotlib
+Requires-Dist: astropy
+Requires-Dist: extinction
+Requires-Dist: requests
+Requires-Dist: lxml
+Requires-Dist: sphinx-rtd-theme
+Requires-Dist: sphinx-tabs
+Requires-Dist: bilby
+Requires-Dist: regex
+Requires-Dist: sncosmo
+Requires-Dist: afterglowpy
+Provides-Extra: all
+Requires-Dist: nestle; extra == "all"
+Requires-Dist: sherpa; extra == "all"
+Requires-Dist: scikit-learn; extra == "all"
+Requires-Dist: PyQt5; extra == "all"
+Requires-Dist: lalsuite; extra == "all"
+Requires-Dist: kilonova-heating-rate; extra == "all"
+Requires-Dist: redback-surrogates; extra == "all"
+Requires-Dist: kilonovanet; extra == "all"
+Requires-Dist: astroquery; extra == "all"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 [![Documentation Status](https://readthedocs.org/projects/redback/badge/?version=latest)](https://redback.readthedocs.io/en/latest/?badge=latest)
 ![Python package](https://github.com/nikhil-sarin/redback/workflows/Python%20application/badge.svg)
@@ -45,9 +82,12 @@ Simulate single transients or populations or simulate a full survey including no
 
 ### Contributing
 If you are interested in contributing please join the redback 
-[slack](https://join.slack.com/t/redback-group/shared_invite/zt-21rsoa26s-kibI8MiA1JiIKM0wCMp5rQ)
+[slack](https://join.slack.com/t/redback-group/shared_invite/zt-2503mmkaq-EMEAgz7i3mY0pg1o~VUdqw)
 and email [Nikhil Sarin](mailto:nikhil.sarin@su.se?subject=Contributing%20to%20redback).
 
 To make changes to redback, we require users to use a merge request system. 
 
-
+### User/Dev calls
+We have regular calls for users and developers. 
+These include tutorials on specific redback functionality as well as discussions of new features/feature requests, 
+and Q/A. Please join the slack to get details of these calls.

{redback-1.0.1 → redback-1.0.3}/README.md

@@ -30,9 +30,12 @@ Simulate single transients or populations or simulate a full survey including no
 
 ### Contributing
 If you are interested in contributing please join the redback 
-[slack](https://join.slack.com/t/redback-group/shared_invite/zt-21rsoa26s-kibI8MiA1JiIKM0wCMp5rQ)
+[slack](https://join.slack.com/t/redback-group/shared_invite/zt-2503mmkaq-EMEAgz7i3mY0pg1o~VUdqw)
 and email [Nikhil Sarin](mailto:nikhil.sarin@su.se?subject=Contributing%20to%20redback).
 
 To make changes to redback, we require users to use a merge request system. 
 
-
+### User/Dev calls
+We have regular calls for users and developers. 
+These include tutorials on specific redback functionality as well as discussions of new features/feature requests, 
+and Q/A. Please join the slack to get details of these calls.

{redback-1.0.1 → redback-1.0.3}/redback/__init__.py

@@ -2,3 +2,7 @@ from redback import analysis, constants, get_data, redback_errors, priors, resul
     transient_models, utils, photosphere, sed, interaction_processes, constraints, plotting, model_library, simulate_transients
 from redback.transient import afterglow, kilonova, prompt, supernova, tde
 from redback.sampler import fit_model
+from redback.utils import setup_logger
+
+__version__ = "1.0.2"
+setup_logger(log_level='info')

{redback-1.0.1 → redback-1.0.3}/redback/constraints.py

@@ -2,6 +2,7 @@ import numpy as np
 import redback.eos as eos
 from redback.constants import *
 from redback.utils import calc_tfb
+from scipy.interpolate import interp1d
 
 def slsn_constraint(parameters):
     """
@@ -23,7 +24,7 @@ def slsn_constraint(parameters):
     neutrino_energy = 1e51
     total_energy = kinetic_energy + neutrino_energy
     # ensure rotational energy is greater than total output energy
-    converted_parameters['erot_constraint'] = rotational_energy - total_energy
+    converted_parameters['erot_constraint'] = total_energy/rotational_energy
     # ensure t_nebula is greater than 100 days
     converted_parameters['t_nebula_min'] = tnebula - 100
     return converted_parameters
@@ -43,7 +44,7 @@ def basic_magnetar_powered_sn_constraints(parameters):
     kinetic_energy = 0.5 * mej * vej**2
     rotational_energy = 2.6e52 * (mass_ns/1.4)**(3./2.) * p0**(-2)
     # ensure rotational energy is greater than total output energy
-    converted_parameters['erot_constraint'] = rotational_energy - kinetic_energy
+    converted_parameters['erot_constraint'] = kinetic_energy/rotational_energy
     return converted_parameters
 
 def general_magnetar_powered_sn_constraints(parameters):
@@ -61,9 +62,24 @@ def general_magnetar_powered_sn_constraints(parameters):
     tau = parameters['tsd']
     rotational_energy = 2*l0*tau
     # ensure rotational energy is greater than total output energy
-    converted_parameters['erot_constraint'] = rotational_energy - kinetic_energy
+    converted_parameters['erot_constraint'] = kinetic_energy/rotational_energy
     return converted_parameters
     
+def vacuum_dipole_magnetar_powered_supernova_constraints(parameters):
+    """
+    Constraint so that magnetar rotational energy is smaller than some number
+
+    :param parameters: dictionary of parameters
+    :return: converted_parameters dictionary where the violated samples are thrown out
+    """
+    converted_parameters = parameters.copy()
+    l0 = parameters['l0']
+    tau = parameters['tau_sd']
+    rotational_energy = l0*tau
+    # ensure rotational energy is less than the maximum spin down energy
+    converted_parameters['erot_constraint'] = rotational_energy/1e53
+    return converted_parameters        
+    
 def general_magnetar_powered_supernova_constraints(parameters):
     """
     Constraint so that magnetar rotational energy is smaller than some number
@@ -77,7 +93,7 @@ def general_magnetar_powered_supernova_constraints(parameters):
     nn = parameters['nn']    
     rotational_energy = (nn-1)*l0*tau/2.0
     # ensure rotational energy is less than the maximum spin down energy
-    converted_parameters['erot_constraint'] = 1e53 - rotational_energy
+    converted_parameters['erot_constraint'] = rotational_energy/1e53
     return converted_parameters    
 
 def tde_constraints(parameters):
@@ -91,7 +107,7 @@ def tde_constraints(parameters):
     rp = parameters['pericenter_radius']
     mass_bh = parameters['mass_bh']
     schwarzchild_radius = (2 * graviational_constant * mass_bh * solar_mass /(speed_of_light**2))/au_cgs
-    converted_parameters['disruption_radius'] = rp - schwarzchild_radius
+    converted_parameters['disruption_radius'] = schwarzchild_radius/rp
     return converted_parameters
 
 def gaussianrise_tde_constraints(parameters):
@@ -103,13 +119,11 @@ def gaussianrise_tde_constraints(parameters):
     converted_parameters = parameters.copy()
     ms = parameters['stellar_mass']
     mbh6 = parameters['mbh_6']
-    etamin = 0.01*(ms**(-7./15.))*(mbh6**(2./3.))
     betamax = 12.*(ms**(7./15.))*(mbh6**(-2./3.))
     tfb = calc_tfb(binding_energy_const=0.8, mbh_6=mbh6,stellar_mass=ms)/86400
     tfb_obs = tfb * (1 + parameters['redshift'])
-    converted_parameters['eta_low'] = converted_parameters['eta'] - etamin
-    converted_parameters['beta_high'] = betamax - converted_parameters['beta']
-    converted_parameters['tfb_max'] = tfb_obs - converted_parameters['peak_time']
+    converted_parameters['beta_high'] = converted_parameters['beta']/betamax
+    converted_parameters['tfb_max'] = converted_parameters['peak_time']/tfb_obs
     return converted_parameters
 
 def nuclear_burning_constraints(parameters):
@@ -126,7 +140,7 @@ def nuclear_burning_constraints(parameters):
     kinetic_energy = 0.5 * mej * (vej / 2.0) ** 2
     excess_constant = -(56.0 / 4.0 * 2.4249 - 53.9037) / proton_mass * mev_cgs
     emax = excess_constant * mej * fnickel
-    converted_parameters['emax_constraint'] = emax - kinetic_energy
+    converted_parameters['emax_constraint'] = kinetic_energy/emax
     return converted_parameters
 
 def simple_fallback_constraints(parameters):
@@ -149,7 +163,7 @@ def simple_fallback_constraints(parameters):
     neutrino_energy = 1e51
     total_energy = e_fallback + neutrino_energy
     # ensure total energy is greater than kinetic energy
-    converted_parameters['en_constraint'] = total_energy - kinetic_energy
+    converted_parameters['en_constraint'] = kinetic_energy/total_energy
     # ensure t_nebula is greater than 100 days
     converted_parameters['t_nebula_min'] = tnebula - 100
     return converted_parameters
@@ -162,15 +176,18 @@ def csm_constraints(parameters):
     :param parameters: dictionary of parameters
     :return: converted_parameters dictionary where the violated samples are thrown out
     """
-    from redback.utils import get_csm_properties
     converted_parameters = parameters.copy()
     mej = parameters['mej']
     csm_mass = parameters['csm_mass']
     kappa = parameters['kappa']
     r0 = parameters['r0']
     vej = parameters['vej']
-    nn = parameters.get('nn', np.ones(len(mej)) * 12.)
-    delta = parameters.get('delta', np.ones(len(mej)))
+    if hasattr(parameters['mej'], "__len__"):
+        nn = parameters.get('nn', np.ones(len(mej)) * 8.)
+        delta = parameters.get('delta', np.ones(len(mej)))
+    else:
+        nn = parameters.get('nn', 12.)
+        delta = parameters.get('delta', 0.)
     eta = parameters['eta']
     rho = parameters['rho']
 
@@ -180,12 +197,16 @@ def csm_constraints(parameters):
     vej = vej * km_cgs
     Esn = 3. * vej ** 2 * mej / 10.
 
-    AA = np.zeros(len(mej))
-    Bf = np.zeros(len(mej))
-    for x in range(len(mej)):
-        csm_properties = get_csm_properties(nn[x], eta[x])
-        AA[x] = csm_properties.AA
-        Bf[x] = csm_properties.Bf
+    ns = [6, 7, 8, 9, 10, 12, 14]
+    Bfs = [1.377, 1.299, 1.267, 1.250, 1.239, 1.226, 1.218]
+    As = [0.62, 0.27, 0.15, 0.096, 0.067, 0.038, 0.025]
+
+    Bf_func = interp1d(ns, Bfs)
+    A_func = interp1d(ns, As)
+
+    Bf = Bf_func(nn)
+    AA = A_func(nn)
+
     qq = rho * r0 ** eta
     # outer CSM shell radius
     radius_csm = ((3.0 - eta) / (4.0 * np.pi * qq) * csm_mass + r0 ** (3.0 - eta)) ** (
@@ -203,14 +224,14 @@ def csm_constraints(parameters):
                    (3.0 - delta) * (nn - 3.0) * mej) ** ((nn - 5.0) / 2.0))
 
     tshock = ((radius_csm - r0) / Bf / (AA * g_n / qq) ** (
-                       1. / (nn - eta))) ** ((nn - eta) /(nn - 3))
+                       1. / (nn - eta))) ** ((nn - eta) / (nn - 3))
 
-    diffusion_time = np.sqrt(2. * kappa * mass_csm_threshold /(vej * 13.7 * 3.e10))
+    diffusion_time = np.sqrt(2. * kappa * mass_csm_threshold / (vej * 13.7 * 3.e10))
     # ensure shock crossing time is greater than diffusion time
-    # converted_parameters['shock_time'] = tshock - diffusion_time
+    converted_parameters['shock_time'] = diffusion_time/tshock
     # ensure photospheric radius is within the csm i.e., r_photo < radius_csm and r_photo > r0
-    converted_parameters['photosphere_constraint_1'] = radius_csm - r_photosphere
-    converted_parameters['photosphere_constraint_2'] = r_photosphere - r0
+    converted_parameters['photosphere_constraint_1'] = r_photosphere/radius_csm
+    converted_parameters['photosphere_constraint_2'] = r0/r_photosphere
     return converted_parameters
 
 def piecewise_polytrope_eos_constraints(parameters):

{redback-1.0.1 → redback-1.0.3}/redback/eos.py

@@ -78,6 +78,7 @@ class PiecewisePolytrope(object):
         radius, mass, k2 = lalsim.SimNeutronStarTOVODEIntegrate(central_pressure, polytrope)
 
         Lambda = (2 / 3) * k2 * (cc.c.si.value ** 2 * radius / (cc.G.si.value * mass)) ** 5
+        mass = mass / cc.M_sun.si.value
         return mass, Lambda
 
     def lambda_array_of_central_pressure(self, central_pressure_array, maximum_mass_lower_limit=2.01):

{redback-1.0.1 → redback-1.0.3}/redback/get_data/fink.py

@@ -45,7 +45,7 @@ class FinkDataGetter(DataGetter):
         :return: The fink raw data url.
         :rtype: str
         """
-        return "https://fink-portal.org/api/v1/objects"
+        return "https://api.fink-portal.org/api/v1/objects"
 
     @property
     def objectId(self) -> str:

{redback-1.0.1 → redback-1.0.3}/redback/get_data/lasair.py

@@ -58,8 +58,8 @@ class LasairDataGetter(DataGetter):
                 f"Are you sure you are using the right alias?")
         data = pd.read_html(self.url)
         data = data[1]
-        data['diff_magnitude'] = [data['magpsf'].iloc[x].split(" ")[0] for x in range(len(data))]
-        data['diff_magnitude_error'] = [data['magpsf'].iloc[x].split(" ")[-1] for x in range(len(data))]
+        data['diff_magnitude'] = [data['unforced mag'].iloc[x].split(" ")[0] for x in range(len(data))]
+        data['diff_magnitude_error'] = [data['unforced mag'].iloc[x].split(" ")[-1] for x in range(len(data))]
 
         logger.warning('Using the difference magnitude to calculate quantities. '
                        'Reduce the data yourself if you would like to use a reference magnitude')
@@ -67,7 +67,6 @@ class LasairDataGetter(DataGetter):
         # Change the dataframe to the correct raw dataframe format
         del data['UTC']
         del data['images']
-        del data['magpsf']
         data.to_csv(self.raw_file_path, index=False)
         logger.info(f"Retrieved data for {self.transient}.")
 
@@ -83,7 +82,7 @@ class LasairDataGetter(DataGetter):
             return pd.read_csv(self.processed_file_path)
 
         raw_data = pd.read_csv(self.raw_file_path)
-        raw_data = raw_data[raw_data['difference flux status'] != 'limit']
+        raw_data = raw_data[raw_data['unforced mag status'] != 'limit']
         lasair_to_general_bands = {"g": "ztfg", "r": "ztfr", "i":'ztfi'}
         processed_data = pd.DataFrame()
 

{redback-1.0.1 → redback-1.0.3}/redback/get_data/swift.py

@@ -199,9 +199,9 @@ class SwiftDataGetter(GRBDataGetter):
         driver = fetch_driver()
         try:
             driver.get(self.grb_website)
-            driver.find_element_by_xpath("//select[@name='xrtsub']/option[text()='no']").click()
+            driver.find_element("xpath", "//select[@name='xrtsub']/option[text()='no']").click()
             time.sleep(20)
-            driver.find_element_by_id("xrt_DENSITY_makeDownload").click()
+            driver.find_element("id","xrt_DENSITY_makeDownload").click()
             time.sleep(20)
             grb_url = driver.current_url
             # scrape the data
@@ -227,19 +227,19 @@ class SwiftDataGetter(GRBDataGetter):
             # select option for BAT bin_size
             bat_binning = 'batxrtbin'
             if check_element(driver, bat_binning):
-                driver.find_element_by_xpath("//select[@name='batxrtbin']/option[text()='SNR 4']").click()
+                driver.find_element("xpath", "//select[@name='batxrtbin']/option[text()='SNR 4']").click()
             # select option for subplot
             subplot = "batxrtsub"
             if check_element(driver, subplot):
-                driver.find_element_by_xpath("//select[@name='batxrtsub']/option[text()='no']").click()
+                driver.find_element("xpath","//select[@name='batxrtsub']/option[text()='no']").click()
             # Select option for flux density
             flux_density1 = "batxrtband1"
             flux_density0 = "batxrtband0"
             if (check_element(driver, flux_density1)) and (check_element(driver, flux_density0)):
-                driver.find_element_by_xpath(".//*[@id='batxrtband1']").click()
-                driver.find_element_by_xpath(".//*[@id='batxrtband0']").click()
+                driver.find_element("xpath",".//*[@id='batxrtband1']").click()
+                driver.find_element("xpath",".//*[@id='batxrtband0']").click()
             # Generate data file
-            driver.find_element_by_xpath(".//*[@id='batxrt_XRTBAND_makeDownload']").click()
+            driver.find_element("xpath",".//*[@id='batxrt_XRTBAND_makeDownload']").click()
             time.sleep(20)
             grb_url = driver.current_url
             driver.quit()

{redback-1.0.1 → redback-1.0.3}/redback/interaction_processes.py

@@ -165,8 +165,6 @@ class CSMDiffusion(object):
         # photosphere radius
         r_photosphere = self.r_photosphere
 
-        tau_diff = (self.kappa * self.csm_mass) / (13.8 * speed_of_light * r_photosphere) / day_to_s
-
         # mass of the optically thick CSM (tau > 2/3).
         mass_csm_threshold = self.mass_csm_threshold
 
@@ -180,7 +178,7 @@ class CSMDiffusion(object):
         lu = len(uniq_times)
 
         num = int(round(timesteps / 2.0))
-        lsp = np.logspace(np.log10(tau_diff /self.dense_times[-1]) + minimum_log_spacing, 0, num)
+        lsp = np.logspace(np.log10(t0 /self.dense_times[-1]) + minimum_log_spacing, 0, num)
         xm = np.unique(np.concatenate((lsp, 1 - lsp)))
 
         int_times = tb + (uniq_times.reshape(lu, 1) - tb) * xm
@@ -192,7 +190,6 @@ class CSMDiffusion(object):
 
         uniq_lums = np.trapz(int_args, int_times, axis=1)
         uniq_lums *= np.exp(-int_tes/t0)/t0
-
         new_lums = uniq_lums[np.searchsorted(uniq_times, self.time)]
         return new_lums