Merge pull request #100 from kadrlica/lsst_sims

Merge updates for LSST DP0 simulations

.github/workflows/python-package.yml

@@ -8,6 +8,7 @@ name: build
 on:
   push:
   pull_request:
+  workflow_dispatch:
   schedule:
   - cron: '0 0 1 * *'
 

ugali/analysis/imf.py

@@ -27,7 +27,7 @@ def integrate(self, mass_min, mass_max, log_mode=True, weight=False, steps=10000
         -----------
         mass_min: minimum mass bound for integration (solar masses)
         mass_max: maximum mass bound for integration (solar masses)
-        log_mode[True]: use logarithmic steps in stellar mass as oppose to linear
+        log_mode[True]: use logarithmic steps in stellar mass as opposed to linear
         weight[False]: weight the integral by stellar mass
         steps: number of numerical integration steps
 

ugali/isochrone/dartmouth.py

@@ -103,8 +103,8 @@
 
 class Dotter2008(Isochrone):
     """
-    KCB: currently inheriting from PadovaIsochrone because there are 
-    several useful functions where we would basically be copying code.
+    Dartmouth isochrones from Dotter et al. 2008 (https://arxiv.org/abs/0804.4473)
+    http://stellar.dartmouth.edu
     """
     _dirname =  os.path.join(get_iso_dir(),'{survey}','dotter2008')
     #_zsolar = 0.0163 

ugali/isochrone/model.py

@@ -96,9 +96,9 @@ class IsochroneModel(Model):
     """ Abstract base class for dealing with isochrone models. """
 
     _params = odict([
-        ('distance_modulus', Parameter(15.0, [10.0, 30.0]) ),
+        ('distance_modulus', Parameter(15.0, [10.0, 30.0]) ), # m-M
         ('age',              Parameter(10.0, [0.1, 15.0]) ),  # Gyr
-        ('metallicity',      Parameter(0.0002, [0.0,0.02]) ),
+        ('metallicity',      Parameter(0.0002, [0.0,0.02]) ), # Z_ini
     ])
     _mapping = odict([
         ('mod','distance_modulus'),
@@ -385,7 +385,7 @@ def absolute_magnitude_martin(self, richness=1, steps=1e4, n_trials=1000, mag_br
 
         Returns:
         --------
-        med,lo,hi : Total absolute magnitude interval
+        med,[lo,hi] : Total absolute magnitude interval
         """
         # ADW: This function is not quite right. It should restrict
         # the catalog to the obsevable space using the mask in each
@@ -398,6 +398,10 @@ def absolute_magnitude_martin(self, richness=1, steps=1e4, n_trials=1000, mag_br
         params.update(band_1='g',band_2='r',survey='sdss')
         iso = self.__class__(**params)
 
+        # ADW: 2022-09-18: There are now direct transformation
+        # equations from DES to Johnson V-band...
+        # Appendix B.5: https://arxiv.org/abs/2101.05765
+
         # Analytic part (below detection threshold)
         # g, r are absolute magnitudes
         mass_init, mass_pdf, mass_act, sdss_g, sdss_r = iso.sample(mass_steps = steps)
@@ -440,10 +444,15 @@ def simulate(self, stellar_mass, distance_modulus=None, **kwargs):
         """
         if distance_modulus is None: distance_modulus = self.distance_modulus
         # Total number of stars in system
-        n = int(round(stellar_mass / self.stellar_mass()))
-        f_1 = scipy.interpolate.interp1d(self.mass_init, self.mag_1)
-        f_2 = scipy.interpolate.interp1d(self.mass_init, self.mag_2)
-        mass_init_sample = self.imf.sample(n, np.min(self.mass_init), np.max(self.mass_init), **kwargs)
+        richness = stellar_mass / self.stellar_mass()
+        n = int(round(richness))
+        #ADW 2022-08-28: Should this really be a Poisson sample of the richness?
+        #n = scipy.stats.poisson(richness).rvs()
+
+        mass_init,mag_1,mag_2 = self.mass_init, self.mag_1, self.mag_2
+        f_1 = scipy.interpolate.interp1d(mass_init, mag_1)
+        f_2 = scipy.interpolate.interp1d(mass_init, mag_2)
+        mass_init_sample = self.imf.sample(n, np.min(mass_init), np.max(mass_init), **kwargs)
         mag_1_sample, mag_2_sample = f_1(mass_init_sample), f_2(mass_init_sample) 
         return mag_1_sample + distance_modulus, mag_2_sample + distance_modulus
 
@@ -907,8 +916,11 @@ def pdf(self, mag_1, mag_2, mag_err_1, mag_err_2,
 
 
     def raw_separation(self,mag_1,mag_2,steps=10000):
-        """ 
-        Calculate the separation in magnitude-magnitude space between points and isochrone. Uses a dense sampling of the isochrone and calculates the metric distance from any isochrone sample point.
+        """
+        Calculate the separation in magnitude-magnitude space between
+        points and isochrone. Uses a dense sampling of the isochrone
+        and calculates the metric distance from any isochrone sample
+        point.
 
         Parameters:
         -----------
@@ -1074,11 +1086,14 @@ def create_grid(self,abins=None,zbins=None):
         if abins is None and zbins is None:
             filenames = glob.glob(self.get_dirname()+'/%s_*.dat'%(self._prefix))
             data = np.array([self.filename2params(f) for f in filenames])
-            if not len(data):
+            if len(data):
+                arange = np.unique(data[:,0])
+                zrange = np.unique(data[:,1])
+            else:
                 msg = "No isochrone files found in: %s"%self.get_dirname()
-                raise Exception(msg)
-            arange = np.unique(data[:,0])
-            zrange = np.unique(data[:,1])
+                logger.warn(msg)
+                arange = np.array([self.age])
+                zrange = np.array([self.metallicity])
         elif abins is not None and zbins is not None:            
             # Age in units of Gyr
             arange = np.linspace(abins[0],abins[1],abins[2]+1)
@@ -1110,7 +1125,11 @@ def _cache(self,name=None):
         filename = self.get_filename()
         if filename != self.filename:
             self.filename = filename
-            self._parse(self.filename)
+            if not os.path.exists(self.filename):
+                msg = "Filename does not exist: %s"%self.filename
+                logger.warn(msg)
+            else:
+                self._parse(self.filename)
 
     def _parse(self,filename):
         raise Exception("Must be implemented by subclass.")
@@ -1143,7 +1162,7 @@ def download(self,age=None,metallicity=None,outdir=None,force=False):
         Parameters
         ----------
         age         : age in (Gyr)
-        metallicity : Z
+        metallicity : initial metallicity, Z
         outdir      : output directory (default to current directory)
         force       : force overwrite of file
 

ugali/isochrone/parsec.py

@@ -34,6 +34,7 @@
         ('ps1' ,'tab_mag_odfnew/tab_mag_panstarrs1.dat'),
         ('acs_wfc' ,'tab_mag_odfnew/tab_mag_acs_wfc.dat'),
         ('lsst', 'tab_mag_odfnew/tab_mag_lsst.dat'),
+        ('lsst_dp0', 'tab_mag_odfnew/tab_mag_lsstDP0.dat'),
 ])
 
 photname_dict = odict([
@@ -42,6 +43,7 @@
         ('ps1' ,'Pan-STARRS1'),
         ('acs_wfc','HST/ACS'),
         ('lsst', 'LSST'),
+        ('lsst_dp0', 'LSST'),
 ])
 
 # Commented options may need to be restored for older version/isochrones.
@@ -155,6 +157,8 @@
                #'.cgifields': 'dust_sourceM',
                }
 
+defaults_36 = dict(defaults_33,cmd_version=3.6)
+
 class ParsecIsochrone(Isochrone):
     """ Base class for PARSEC-style isochrones. """
 
@@ -242,7 +246,7 @@ def query_server(self,outfile,age,metallicity):
         urlopen(url,timeout=2)
 
         q = urlencode(params).encode('utf-8')
-        logger.debug(url+'?'+q)
+        logger.debug("%s?%s"%(url,q))
         c = str(urlopen(url, q).read())
         aa = re.compile('output\d+')
         fname = aa.findall(c)
@@ -256,49 +260,93 @@ def query_server(self,outfile,age,metallicity):
         cmd = 'wget --progress dot:binary %s -O %s'%(out,outfile)
         logger.debug(cmd)
         stdout = subprocess.check_output(cmd,shell=True,stderr=subprocess.STDOUT)
-        logger.debug(stdout)
+        logger.debug(str(stdout))
 
         return outfile
 
     @classmethod
-    def verify(cls, filename, survey, age, metallicity):
-        age = age*1e9
-        nlines=15
+    def parse_header(cls, filename, nlines=15):
+        header = dict(
+            photname = None,
+            columns = None
+        )
+
         with open(filename,'r') as f:
             lines = [f.readline() for i in range(nlines)]
-            if len(lines) < nlines:
-                msg = "Incorrect file size"
-                raise Exception(msg)
 
-            for i,l in enumerate(lines):
-                if l.startswith('# Photometric system:'): break
-            else:
-                msg = "Incorrect file header"
-                raise Exception(msg)
+        if len(lines) < nlines:
+            msg = "Incorrect file size"
+            raise Exception(msg)
 
-            try:
-                s = lines[i].split()[3]
-                assert photname_dict[survey] == s
-            except:
-                msg = "Incorrect survey:\n"+lines[i]
-                raise Exception(msg)
+        for i,l in enumerate(lines):
+            if l.startswith('# Photometric system:'): 
+                try:    header['photname'] = lines[i].split()[3]
+                except: header['photname'] = None
+            if not l.startswith('# '): break
 
-            try:
-                z = lines[-1].split()[0]
-                assert np.allclose(metallicity,float(z),atol=1e-5)
-            except:
-                msg = "Metallicity does not match:\n"+lines[-1]
-                raise Exception(msg)
+        header['columns'] = lines[i-1].split()[1:]
 
-            try:
-                a = lines[-1].split()[1]
-                # Need to deal with age or log-age
-                assert (np.allclose(age,float(a),atol=1e-2) or
-                        np.allclose(np.log10(age),float(a),atol=1e-2))
-            except:
-                msg = "Age does not match:\n"+lines[-1]
+        for k,v in header.items():
+            if v is None: 
+                msg = "File header missing: '%s'"%k
                 raise Exception(msg)
 
+        return header, lines
+
+    @classmethod
+    def verify(cls, filename, survey, age, metallicity):
+        """Verify that the isochrone file matches the isochrone
+        parameters. Used mostly for verifying the integrity of 
+        a download.
+
+        Parameters
+        ----------
+        filename    : the downloaded filename 
+        survey      : the survey (photometric system) of the download
+        age         : the requested age of the system
+        metallicity : the requested metallicity
+
+        Returns
+        -------
+        None
+        """
+        age = age*1e9
+        nlines=15
+        header, lines = cls.parse_header(filename,nlines=nlines)
+
+        try:
+            assert photname_dict[survey] == header['photname']
+        except:
+            msg = "Incorrect survey:\n"+header['photname']
+            raise Exception(msg)
+
+        try:
+            try: zidx = header['columns'].index('Zini')
+            except ValueError: zidx = 0
+            z = float(lines[-1].split()[zidx])
+            assert np.allclose(metallicity,z,atol=1e-5)
+        except:
+            msg = "Metallicity does not match:\n"+lines[-1]
+            raise Exception(msg)
+
+        try:
+            # Need to deal with age or log-age
+            names = ['log(age/yr)', 'logAge', 'Age']
+            for name in names:
+                try: 
+                    aidx = header['columns'].index(name)
+                    break
+                except ValueError: 
+                    aidx = 1
+            if aidx < 0: aidx = 1
+
+            a = lines[-1].split()[aidx]
+            assert (np.allclose(age,float(a),atol=1e-2) or
+                    np.allclose(np.log10(age),float(a),atol=1e-2))
+        except:
+            msg = "Age does not match:\n"+lines[-1]
+            raise Exception(msg)
+
 
 class Bressan2012(ParsecIsochrone):
     _dirname =  os.path.join(get_iso_dir(),'{survey}','bressan2012')
@@ -403,7 +451,7 @@ class Marigo2017(ParsecIsochrone):
         ('hb_spread',0.1,'Intrinisic spread added to horizontal branch'),
         )
 
-    download_defaults = copy.deepcopy(defaults_31)
+    download_defaults = copy.deepcopy(defaults_36)
     download_defaults['isoc_kind'] = 'parsec_CAF09_v1.2S_NOV13'
 
     columns = dict(
@@ -442,24 +490,38 @@ class Marigo2017(ParsecIsochrone):
                 (27,('y',float)),
                 (28,('w',float)),
                 ]),
-        lsst = odict([
-                (2, ('mass_init',float)),
-                (3, ('mass_act',float)),
-                (4, ('log_lum',float)),
-                (7, ('stage',int)),
-                (23,('u',float)),
-                (24,('g',float)),
-                (25,('r',float)),
-                (26,('i',float)),
-                (27,('z',float)),
-                (28,('Y',float)),
+        lsst_dp0 = odict([
+                (3, ('mass_init',float)),
+                (5, ('mass_act',float)),
+                (6, ('log_lum',float)),
+                (9, ('stage',int)),
+                (25,('u',float)),
+                (26,('g',float)),
+                (27,('r',float)),
+                (28,('i',float)),
+                (29,('z',float)),
+                (30,('Y',float)),
                 ]),
         )
+    columns['lsst'] = copy.deepcopy(columns['lsst_dp0'])
+
+    def _find_column_numbers(self):
+        """ Map from the isochrone column names to the column numbers. """
+        header,lines = self.parse_header(self.filename)
+        columns = header['columns']
 
     def _parse(self,filename):
-        """Reads an isochrone file in the Padova (Marigo et al. 2017)
+        """Reads an isochrone file in the Marigo et al. 2017
         format. Creates arrays with the initial stellar mass and
         corresponding magnitudes for each step along the isochrone.
+
+        Parameters:
+        -----------
+        filename : name of isochrone file to parse
+
+        Returns:
+        --------
+        None
         """
         try:
             columns = self.columns[self.survey.lower()]
@@ -471,7 +533,7 @@ def _parse(self,filename):
         self.data = np.genfromtxt(filename,**kwargs)
         # cut out anomalous point:
         # https://github.com/DarkEnergySurvey/ugali/issues/29
-        self.data = self.data[self.data['stage'] != 9]
+        self.data = self.data[~np.in1d(self.data['stage'], [9])]
 
         self.mass_init = self.data['mass_init']
         self.mass_act  = self.data['mass_act']