nucleardatapy 0.2.0__py3-none-any.whl

nucleardatapy/astro/setup_mr.py

@@ -0,0 +1,399 @@
+import math
+import numpy as np  # 1.15.0
+
+import nucleardatapy as nuda
+
+def mr_sources():
+    """
+    Return a list of the astrophysical sources for which a mass is given
+
+    :return: The list of sources.
+    :rtype: list[str].
+    """
+    #
+    if nuda.env.verb: print("\nEnter astro_mr()")
+    #
+    sources = [ 'J0030+0451', 'J0740+6620', 'J0437-4715' ]
+    #
+    #print('sources available in the toolkit:',sources)
+    sources_lower = [ item.lower() for item in sources ]
+    #print('sources available in the toolkit:',sources_lower)
+    #
+    if nuda.env.verb: print("Exit astro_mr()")
+    #
+    return sources, sources_lower
+
+def mr_obss( source ):
+    """
+    Return a list of observations for a given source and print them all on the prompt.
+
+    :param source: The source for which there are different observations.
+    :type source: str.
+    :return: The list of observations. \
+    If source == 'J1614–2230': 1, 2, 3, 4, 5.
+    :rtype: list[str].
+    """
+    #
+    if nuda.env.verb: print("\nEnter astro_mr_source()")
+    #
+    if source.lower()=='j0030+0451':
+        obss = [ 1, 2, 3, 4 ]
+    elif source.lower()=='j0740+6620':
+        obss = [ 1, 2 ]
+    elif source.lower()=='j0437-4715':
+        obss = [ 1 ]
+    #
+    #print('Observations available in the toolkit:',obss)
+    #
+    if nuda.env.verb: print("Exit astro_mr_source()")
+    #
+    return obss
+
+class setupMR():
+    """
+    Instantiate the observational mass for a given source and obs.
+
+    This choice is defined in the variables `source` and `obs`.
+
+    `source` can chosen among the following ones: 'J1614–2230'.
+
+    `obs` depends on the chosen source.
+
+    :param source: Fix the name of `source`. Default value: 'J1614–2230'.
+    :type source: str, optional. 
+    :param obs: Fix the `obs`. Default value: 1.
+    :type obs: str, optional. 
+
+    **Attributes:**
+    """
+    def __init__(self, source = 'J0030+0451', obs = 1 ):
+        #
+        if nuda.env.verb: print("Enter setupMR()")
+        #
+        # some checks
+        #
+        sources, sources_lower = mr_sources()
+        if source.lower() not in sources_lower:
+            print('Source ',source,' is not in the list of sources.')
+            print('list of sources:',sources)
+            print('-- Exit the code --')
+            exit()
+        self.source = source
+        if nuda.env.verb: print("source:",source)
+        #
+        obss = mr_obss( source = source )
+        if obs not in obss:
+            print('Obs ',obs,' is not in the list of obs.')
+            print('list of obs:',obss)
+            print('-- Exit the code --')
+            exit()
+        self.obs = obs
+        if nuda.env.verb: print("obs:",obs)
+        #
+        # fix `file_in` and some properties of the object
+        #
+        if source.lower()=='j0030+0451':
+            file_in = nuda.param.path_data+'astro/NICER/J0030+0451.dat'
+            if obs==1:
+                #: Attribute providing the full reference to the paper to be citted.
+                self.ref='M.C. Miller, F.K. Lamb, A.J. Dittmann, aet al., ApJL 887, L24 (2019).'
+                #: Attribute providing the label the data is references for figures.
+                self.label = 'J0030 Miller 2019'
+                #: Attribute providing additional notes about the observation.
+                self.note = "write notes about this observation."
+                self.marker = 'o'
+            elif obs==2:
+                #: Attribute providing the full reference to the paper to be citted.
+                self.ref='T.E. Riley, A.L. Watts, S. Bogdanov, P.S. Ray, et al., ApJ 887, L21 (2019).'
+                #: Attribute providing the label the data is references for figures.
+                self.label = 'J0030 Riley 2019'
+                #: Attribute providing additional notes about the observation.
+                self.note = "write notes about this observation."
+                self.marker = 's'
+            elif obs==3:
+                #: Attribute providing the full reference to the paper to be citted.
+                self.ref='S. Vinciguerra, T. Salmi, A.L. Watts, D. Choudhury, et al., ApJ 961, 62 (2024).'
+                #: Attribute providing the label the data is references for figures.
+                self.label = 'J0030 Vinciguerra 2024a'
+                #: Attribute providing additional notes about the observation.
+                self.note = "write notes about this observation."
+                self.marker = 'x'
+            elif obs==4:
+                #: Attribute providing the full reference to the paper to be citted.
+                self.ref='S. Vinciguerra, T. Salmi, A.L. Watts, D. Choudhury, et al., ApJ 961, 62 (2024).'
+                #: Attribute providing the label the data is references for figures.
+                self.label = 'J0030 Vinciguerra 2024b'
+                #: Attribute providing additional notes about the observation.
+                self.note = "write notes about this observation."
+                self.marker = 'x'
+        elif source.lower()=='j0740+6620':
+            file_in = nuda.param.path_data+'astro/NICER/J0740+6620.dat'
+            if obs==1:
+                #: Attribute providing the full reference to the paper to be citted.
+                self.ref='M.C. Miller, F.K. Lamb, A.J. Dittmann, S. Bogdanov, et al., ApJL 918, L28 (2021).'
+                #: Attribute providing the label the data is references for figures.
+                self.label = 'J0740 Miller 2021'
+                #: Attribute providing additional notes about the observation.
+                self.note = "write notes about this observation."
+                self.marker = 'o'
+            elif obs==2:
+                #: Attribute providing the full reference to the paper to be citted.
+                self.ref='T.E. Riley, A.L. Watts, P.S. Ray, S. Bogdanov, et al., ApJL 918, L27 (2021).'
+                #: Attribute providing the label the data is references for figures.
+                self.label = 'J0740 Riley 2021'
+                #: Attribute providing additional notes about the observation.
+                self.note = "write notes about this observation."
+                self.marker = 's'
+        elif source.lower()=='j0437-4715':
+            file_in = nuda.param.path_data+'astro/NICER/J0437-4715.dat'
+            if obs==1:
+                #: Attribute providing the full reference to the paper to be citted.
+                self.ref='D. Choudhury, T. Salmi, S. Vinciguerra, T.E. Riley, et al., ApJL 971, L20 (2024).'
+                #: Attribute providing the label the data is references for figures.
+                self.label = 'J0437 Choudhury 2024'
+                #: Attribute providing additional notes about the observation.
+                self.note = "write notes about this observation."
+                self.marker = 'o'
+        #
+        #: Attribute the observational mass of the source.
+        self.mass = None
+        #: Attribute the positive uncertainty.
+        self.mass_sig_up = None
+        #: Attribute the negative uncertainty.
+        self.mass_sig_lo = None
+        #: Attribute the observational mass of the source.
+        self.rad = None
+        #: Attribute the positive uncertainty.
+        self.rad_sig_up = None
+        #: Attribute the negative uncertainty.
+        self.rad_sig_lo = None
+        #: Attribute latexCite.
+        self.latexCite = None
+        #
+        # read file from `file_in`
+        #
+        with open(file_in,'r') as file:
+            for line in file:
+                if '#' in line: continue
+                ele = line.split(',')
+                #print('ele[0]:',ele[0],' obs:',obs,' ele[:]:',ele[:])
+                if int(ele[0]) == obs:
+                    self.rad = float(ele[1])
+                    self.rad_sig_up = float(ele[2])
+                    self.rad_sig_lo = float(ele[3])
+                    self.mass = float(ele[4])
+                    self.mass_sig_up = float(ele[5])
+                    self.mass_sig_lo = float(ele[6])
+                    #print('ele[7]:',ele[7],' len:',len(ele[7]))
+                    if len(ele[7])>1:
+                        self.comp = float(ele[7])
+                        self.comp_sig_up = float(ele[8])
+                        self.comp_sig_lo = float(ele[9])
+                    else:
+                        self.comp = 0.0
+                        self.comp_sig_up = 1.0
+                        self.comp_sig_lo = 1.0
+                    self.latexCite = ele[10].replace('\n','').replace(' ','')
+        #
+        # compute compactness
+        #
+        # fix the boundary for the masses and the radii:
+        #mmin = self.mass - 3*self.mass_sig_lo
+        #mmax = self.mass + 3*self.mass_sig_up
+        #rmin = self.rad - 3*self.rad_sig_lo
+        #rmax = self.rad + 3*self.rad_sig_up
+        #print('Sch rad of the sun:',nuda.cst.rshsol_si)
+        # construct the distribution of observations in ay
+        #ar = np.linspace(rmin,rmax,300); ar=np.array( ar )
+        #am = np.linspace(mmin,mmax,300); am=np.array( am )
+        ##ac = 0.5 * am / ar
+        #ac = 0.5 * nuda.cst.rshsol_si / 1.e3 * am / ar
+        #ayr = gauss(ar,self.rad,self.rad_sig_up,self.rad_sig_lo); ayr=np.array( ayr )
+        #aym = gauss(am,self.mass,self.mass_sig_up,self.mass_sig_lo); aym=np.array( aym )
+        #ayc = aym * ayr 
+        # determine the centroid and standard deviation for the compactness
+        #noc = sum( ayc )
+        #cenc = sum( ayc*ac )
+        #stdc = sum ( ayc*ac**2 )
+        #self.comp = cenc / noc
+        #self.comp_sig_std = round( math.sqrt( stdc/noc - self.comp**2 ), 3 )
+        #self.comp = round( self.comp, 3)
+        #
+        if nuda.env.verb: print("Exit setupMR()")
+        #
+    #
+    def print_output( self ):
+        """
+        Method which print outputs on terminal's screen.
+        """
+        #
+        if nuda.env.verb: print("Enter print_output()")
+        #
+        print("- Print output:")
+        print("   source:  ",self.source)
+        print("   obs:",self.obs)
+        print("   mass:",self.mass,' in Mo')
+        print("   sigma(mass):",self.mass_sig_up,self.mass_sig_lo,' in Mo')
+        print("   rad:",self.rad,' in km')
+        print("   sigma(mass):",self.rad_sig_up,self.rad_sig_lo,' in km')
+        print("   compactness:",self.comp)
+        print("   sigma(comp):",self.comp_sig_up,self.comp_sig_lo)
+        print("   latexCite:",self.latexCite)
+        print("   ref:    ",self.ref)
+        print("   label:  ",self.label)
+        print("   note:   ",self.note)
+        #
+        if nuda.env.verb: print("Exit print_output()")
+        #
+    #
+    def print_latex( self ):
+        """
+        Method which print outputs in table format (latex) on terminal's screen.
+        """
+        #
+        if nuda.env.verb: print("Enter print_latex()")
+        #
+        if nuda.env.verb_latex:
+            print(rf"- table: {self.source} & {self.obs} & ${{{self.rad:.2f}}}^{{{+self.rad_sig_up}}}_{{{-self.rad_sig_lo}}}$ & ${self.mass:.3f}^{{{+self.mass_sig_up}}}_{{{-self.mass_sig_lo}}}$ & ${self.comp}^{{{+self.comp_sig_up}}}_{{{-self.comp_sig_lo}}}$ & \cite{{{self.latexCite}}} \\\\")
+        else:
+            print(rf"- No  table for source {self.source}. To get  table, write  'verb_table = True' in env.py.")
+        #
+        if nuda.env.verb: print("Exit print_latex()")
+        #
+
+class setupMRAverage():
+    """
+    Instantiate the observational mass for a given source and averaged over obs.
+
+    This choice is defined in the variable `source`.
+
+    `source` can chosen among the following ones: 'J1614–2230'.
+
+    :param source: Fix the name of `source`. Default value: 'J1614–2230'.
+    :type source: str, optional. 
+
+    **Attributes:**
+    """
+    def __init__(self, source = 'J1614–2230', obss = [ 1, 2 ] ):
+        #
+        if nuda.env.verb: print("Enter SetupAstroMRAverage()")
+        #
+        self.source = source
+        self.latexCite = None
+        self.ref = None
+        self.label = source+' average'
+        self.note = 'compute the centroid and standard deviation over several obs. data.'
+        #
+        #obss = mr_obss( source = source )
+        #
+        # search for the boundary for the masses and the radii:
+        mmin = 3.0; mmax = 0.0;
+        rmin = 30.0; rmax = 0.0;
+        cmin = 30.0; cmax = 0.0;
+        for obs in obss:
+            # mass:
+            mr = nuda.setupMR( source = source, obs = obs )
+            mlo = mr.mass - 3*mr.mass_sig_lo
+            mup = mr.mass + 3*mr.mass_sig_up
+            if mlo < mmin: mmin = mlo
+            if mup > mmax: mmax = mup
+            # radius:
+            rlo = mr.rad - 3*mr.rad_sig_lo
+            rup = mr.rad + 3*mr.rad_sig_up
+            if rlo < rmin: rmin = rlo
+            if rup > rmax: rmax = rup
+            # compactness:
+            clo = mr.comp - 3*mr.comp_sig_lo
+            cup = mr.comp + 3*mr.comp_sig_up
+            if clo < cmin: cmin = clo
+            if cup > cmax: cmax = cup
+        # construct the distribution of observations in ay
+        ar = np.linspace(rmin,rmax,300); ar=np.array( ar )
+        am = np.linspace(mmin,mmax,300); am=np.array( am )
+        print('cmax:',cmax)
+        print('cmin:',cmin)
+        ac = np.linspace(cmin,cmax,300); ac=np.array( ac )
+        #ac = 0.5 * nuda.cst.rshsol_si / 1.e3 * am / ar
+        ayr = np.zeros(300); ayr=np.array( ayr )
+        aym = np.zeros(300); aym=np.array( aym )
+        ayc = np.zeros(300); ayc=np.array( ayc )
+        for obs in obss:
+            mr = nuda.setupMR( source = source, obs = obs )
+            ayr += gauss(ar,mr.rad,mr.rad_sig_up,mr.rad_sig_lo)
+            aym += gauss(am,mr.mass,mr.mass_sig_up,mr.mass_sig_lo)
+            ayc += gauss(ac,mr.comp,mr.comp_sig_up,mr.comp_sig_lo)
+        #ayc = aym * ayr 
+        # determine the centroid and standard deviation from the distribution of obs. 
+        nor = sum( ayr )
+        nom = sum( aym )
+        noc = sum( ayc )
+        cenr = sum( ayr*ar )
+        cenm = sum( aym*am )
+        cenc = sum( ayc*ac )
+        stdr = sum ( ayr*ar**2 )
+        stdm = sum ( aym*am**2 )
+        stdc = sum ( ayc*ac**2 )
+        self.rad_cen = cenr / nor
+        self.mass_cen = cenm / nom
+        self.comp_cen = cenc / noc
+        self.rad_sig_std = round( math.sqrt( stdr/nor - self.rad_cen**2 ), 3 )
+        self.mass_sig_std = round( math.sqrt( stdm/nom - self.mass_cen**2 ), 3 )
+        self.comp_sig_std = round( math.sqrt( stdc/noc - self.comp_cen**2 ), 3 )
+        self.rad_cen = round( self.rad_cen, 3)
+        self.mass_cen = round( self.mass_cen, 3)
+        self.comp_cen = round( self.comp_cen, 3)
+        #
+        if nuda.env.verb: print("Exit setupMRAverage()")
+    #
+    def print_output( self ):
+        """
+        Method which print outputs on terminal's screen.
+        """
+        #
+        if nuda.env.verb: print("Enter print_output()")
+        #
+        if nuda.env.verb_output:
+            print("- Print output (average):")
+            print("   source:  ",self.source)
+            print("   mass_cen:",self.mass_cen,' in Mo')
+            print("   mass_sig_std:",self.mass_sig_std,' in Mo')
+            print("   rad_cen:",self.rad_cen,' in km')
+            print("   rad_sig_std:",self.rad_sig_std,' in km')
+            print("   compactness:",self.comp_cen)
+            print("   sigma(comp):",self.comp_sig_std)
+            print("   label:  ",self.label)
+            print("   note:   ",self.note)
+        else:
+            print(f"- No output for source {self.source} (average). To get output, write 'verb_output = True' in env.py.")
+        #
+        if nuda.env.verb: print("Exit print_output()")
+        #
+    #
+    def print_latex( self ):
+        """
+        Method which print outputs in table format (latex) on terminal's screen.
+        """
+        #
+        if nuda.env.verb: print("Enter print_latex()")
+        #
+        if nuda.env.verb_latex:
+            print(rf"- table: {self.source} & av & ${self.rad_cen:.2f}\pm{self.rad_sig_std}$ & ${self.mass_cen:.3f}\pm{self.mass_sig_std}$ & ${self.comp_cen}\pm{self.comp_sig_std}$ & \\\\")
+        else:
+            print(rf"- No table for source {self.source} (average). To get table, write 'verb_latex = True' in env.py.")
+        #
+        if nuda.env.verb: print("Exit print_latex()")
+        #
+
+def gauss( ax, cent, sig_up, sig_lo ):
+    fac = math.sqrt( 2*math.pi )
+    gauss = []
+    for x in ax:
+        if x < cent: 
+            z = ( x - cent ) / sig_lo
+            norm = sig_lo * fac
+        else:
+            z = ( x - cent ) / sig_up
+            norm = sig_up * fac
+        gauss.append( math.exp( -0.5*z**2 ) / norm )
+    return gauss
+

nucleardatapy/astro/setup_mtov.py

@@ -0,0 +1,143 @@
+import math
+import numpy as np  # 1.15.0
+from scipy import special
+
+import nucleardatapy as nuda
+
+def compute_proba_do( amass, mass_cen, sig_up, sig_lo ):
+    fac = math.sqrt( 2.0 )
+    prob = []
+    for m in amass:
+        if m < mass_cen: 
+            z = ( m - mass_cen ) / sig_lo / fac
+            norm = sig_lo * fac
+        else:
+            z = ( m - mass_cen ) / sig_up / fac
+            norm = sig_up * fac
+        prob.append( 0.5 * ( special.erf(z)+1) )
+    return prob
+
+def compute_proba_up( amass, mass_cen, sig_up, sig_lo ):
+    fac = math.sqrt( 2.0 )
+    prob = []
+    for m in amass:
+        if m < mass_cen: 
+            z = ( m - mass_cen ) / sig_lo / fac
+            norm = sig_lo * fac
+        else:
+            z = ( m - mass_cen ) / sig_up / fac
+            norm = sig_up * fac
+        prob.append( 0.5 * ( 1-special.erf(z)) )
+    return prob
+
+class setupMtov():
+    """
+    Instantiate the observational mass for a given source and obs.
+
+    This choice is defined in the variable `source`.
+
+    `source` can chosen among the following ones: 'J1614–2230'.
+
+    :param source: Fix the name of `source`. Default value: 'J1614–2230'.
+    :type source: str, optional. 
+
+    **Attributes:**
+    """
+    def __init__(self, sources_lo = np.array(['J1614–2230']), sources_up = np.array([ 'GW170817' ]) ):
+        #
+        if nuda.env.verb: print("Enter setupMtov()")
+        #
+        # lower bound from neutron star mass observation
+        #
+        self.sources_lo = sources_lo
+        self.sources_up = sources_up
+        if nuda.env.verb: print("sources_lo:",sources_lo)
+        if nuda.env.verb: print("sources_up:",sources_up)
+        #
+        # construct the distribution of masses:
+        self.mass = np.linspace(1.5,3.5,300)
+        #
+        nsources = len(sources_lo)
+        self.proba_lo = np.zeros((nsources,300))
+        self.proba_lo_tot = np.ones(300)
+        self.label_lo = []
+        #
+        for ind,source in enumerate(sources_lo):
+            #print('Call average for source:', source)
+            avmass = nuda.setupMassesAverage( source = source )
+            #print('End of call average')
+            #avmass.print_outputs( )
+            #print('source:',source,' mass:',avmass.mass_cen,' sig_std:',avmass.sig_std )
+            self.proba_lo[ind] = compute_proba_do(self.mass, avmass.mass_cen, avmass.sig_std, avmass.sig_std)
+            self.label_lo.append( str(source) )
+            #print('proba:',self.proba[ind])
+            self.proba_lo_tot = self.proba_lo_tot * self.proba_lo[ind]
+            #
+        self.label_lo_tot = 'Lower boundary'
+        #
+        # upper bound from GW observation
+        #
+        #sources_up = nuda.astro_mup( )[0]
+        #print('Complete list of available sources_up:',sources_up)
+        #
+        #sources_up = [ 'GW170817', 'GW190814' ]
+        #
+        #print('sources_up considered:',sources_up)
+        #
+        nsources = len(sources_up)
+        self.proba_up = np.zeros((nsources,300))
+        self.proba_up_tot = np.ones(300)
+        self.label_up = []
+        #
+        for ind,source in enumerate(sources_up):
+            print('Call average for source:', source)
+            hyps = nuda.astro.mup_hyps( source = source )
+            if source=='GW170817': hyps = [ 3, 4 ]
+            print('   hyps:',hyps)
+            avmup = nuda.setupMupAverage( source = source, hyps = hyps )
+            #print('End of call average')
+            #avmup.print_outputs( )
+            self.proba_up[ind] = compute_proba_up(self.mass, avmup.mup_cen, avmup.sig_std, avmup.sig_std)
+            self.label_up.append( str(source) )
+            self.proba_up_tot = self.proba_up_tot * self.proba_up[ind]
+            #
+        self.label_up_tot = 'Upper boundary'
+        #
+        self.proba_tot = self.proba_lo_tot * self.proba_up_tot
+        self.label_tot = 'Total'
+        #
+        if nuda.env.verb: print("Exit SetupAstroMtov()")
+        #
+    #
+    def print_output( self ):
+        """
+        Method which print outputs on terminal's screen.
+        """
+        print("")
+        #
+        if nuda.env.verb: print("Enter print_output()")
+        #
+        print("- Print output:")
+        print("   sources_lo:  ",self.sources_lo)
+        print("   sources_up:  ",self.sources_up)
+        print("   mass:",self.mass)
+        print("   proba_tot:",self.proba_tot)
+        #
+        if nuda.env.verb: print("Exit print_output()")
+        #
+    #
+    def print_latex( self ):
+        """
+        Method which print outputs in table format (latex) on terminal's screen.
+        """
+        #
+        if nuda.env.verb: print("Enter print_latex()")
+        #
+        if nuda.env.verb_latex:
+            print(rf"- table: {self.sources_lo} & {self.sources_up} \\\\")
+        else:
+            print(rf"- No  table for sources {self.sources_lo} and {self.sources_up}. To get  table, write  'verb_latex = True' in env.py.")
+        #
+        if nuda.env.verb: print("Exit print_latex()")
+        #
+