Add WD Hubeny models

docs/index.rst

@@ -50,21 +50,16 @@ trace if it is necessary.
 Contributing
 ============
 
-Like the `Astropy`_ project, the ``measure_extinction`` is made both by and for its
+Like the `Astropy`_ project, ``measure_extinction`` is made both by and for its
 users.  We accept contributions at all levels, spanning the gamut from fixing a
 typo in the documentation to developing a major new feature. We welcome
 contributors who will abide by the `Python Software Foundation Code of Conduct
 <https://www.python.org/psf/conduct/>`_.
 
 ``measure_extinction`` follows the same workflow and coding guidelines as
-`Astropy`_.  The following pages will help you get started with contributing
-fixes, code, or documentation (no git or GitHub experience necessary):
-
-* `How to make a code contribution <https://docs.astropy.org/en/latest/development/workflow/development_workflow.html>`_
-
-* `Coding Guidelines <https://docs.astropy.org/en/latest/development/codeguide.html>`_
-
-* `Developer Documentation <https://docs.astropy.org/en/latest/index_dev.html>`_
+`Astropy`_.  Take a look at the astropy 
+`developer <https://docs.astropy.org/en/latest/index_dev.html>`_ documentation for
+guidelines.
 
 For the complete list of contributors please see the `measure_extinction
 contributors page on Github

measure_extinction/plotting/plot_spec.py

@@ -397,7 +397,7 @@ def plot_spectrum(
     plt.rc("ytick.minor", width=2)
 
     # create the plot
-    fig, ax = plt.subplots(figsize=(13, 10))
+    fig, ax = plt.subplots(figsize=(10, 8))
 
     # read in and plot all bands and spectra for this star
     if ".dat" not in star:

measure_extinction/stardata.py

@@ -84,9 +84,9 @@
     def read_bands(self, lines, only_bands=None):
         """
         Read the photometric band data from a DAT file
-        and upate class variables.
+        and update class variables.
         Bands are filled in wavelength order to make life
-        easier in subsequent calcuations (interpolations!)
+        easier in subsequent calculations (interpolations!)
 
         Parameters
         ----------
@@ -105,12 +105,21 @@
 
             if (eqpos >= 0) & (pmpos >= 0) & (line[0] != "#"):
                 # check for reference or unit
-                colpos = max((line.find(";"), line.find("#"), line.find("mJy")))
+                colpos = max(
+                    (
+                        line.find(";"),
+                        line.find("#"),
+                        line.find("mJy"),
+                        line.find("ABmag"),
+                    )
+                )
                 if colpos == -1:
                     colpos = len(line)
                 # if there is both a reference and a unit
-                elif line.find(";") != -1 and line.find("mJy") != -1:
-                    colpos = min(line.find(";"), line.find("mJy"))
+                elif line.find(";") != -1 and (
+                    line.find("mJy") != -1 or line.find("ABmag") != -1
+                ):
+                    colpos = min(line.find(";"), line.find("mJy"), line.find("ABmag"))
                 band_name = line[0:eqpos].strip()
 
                 save_band = False
@@ -127,6 +136,8 @@
                     # units
                     if line.find("mJy") >= 0:
                         self.band_units[band_name] = "mJy"
+                    elif line.find("ABmag") >= 0:
+                        self.band_units[band_name] = "ABmag"
                     else:
                         self.band_units[band_name] = "mag"
 
@@ -183,32 +194,47 @@
         _n_wfpc2_bands = len(_wfpc2_vegamag)
         _wfpc2_band_zeromag_fluxes = np.zeros(_n_wfpc2_bands)
 
-        # zeromag Vega flux not given in standard WFPC2 documenation
+        # zeromag Vega flux not given in standard WFPC2 documentation
         # instead the flux and Vega magnitudes are given for 1 DN/sec
         # the following code coverts these numbers to zeromag Vega fluxes
         for i in range(_n_wfpc2_bands):
             _wfpc2_band_zeromag_fluxes[i] = _wfpc2_photflam[i] * (
                 10 ** (0.4 * _wfpc2_vegamag[i])
             )
 
-        # WFC3 bands
+        # WFC3 bands - updated for 2020 solutions  Assuming UVIS1
         _wfc3_band_names = [
             "WFC3_F275W",
             "WFC3_F336W",
             "WFC3_F475W",
+            "WFC3_F625W",
+            "WFC3_F775W",
             "WFC3_F814W",
             "WFC3_F110W",
             "WFC3_F160W",
         ]
-        _wfc3_band_waves = np.array([0.2710, 0.3355, 0.4772, 0.8053, 1.1534, 1.5369])
+        _wfc3_band_waves = np.array(
+            [0.2710, 0.3355, 0.4773, 0.6243, 0.7651, 0.8053, 1.1534, 1.5369]
+        )
         _wfc3_photflam = np.array(
-            [3.186e-18, 1.267e-18, 2.458e-19, 1.477e-19, 1.53e-20, 1.93e-20]
+            [
+                3.223e-18,
+                1.286e-18,
+                2.498e-19,
+                1.723e-19,
+                2.093e-18,
+                1.477e-19,
+                1.53e-20,
+                1.93e-20,
+            ]
+        )
+        _wfc3_vegamag = np.array(
+            [22.676, 23.526, 25.809, 25.374, 24.84, 24.712, 26.063, 24.695]
         )
-        _wfc3_vegamag = np.array([22.331, 23.513, 25.809, 24.712, 26.063, 24.695])
         _n_wfc3_bands = len(_wfc3_vegamag)
         _wfc3_band_zeromag_fluxes = np.zeros(_n_wfc3_bands)
 
-        # zeromag Vega flux not given in standard WFPC2 documenation
+        # zeromag Vega flux not given in standard WFC3 documentation
         # instead the flux and Vega magnitudes are given for 1 DN/sec
         # the following code coverts these numbers to zeromag Vega fluxes
         for i in range(_n_wfc3_bands):
@@ -464,6 +490,28 @@
                         0.5 * (_flux2 - _flux1),
                     )
                     self.band_waves[pband_name] = poss_bands[pband_name][1]
+                elif _mag_vals[2] == "ABmag":
+                    _flux1_nu = np.power(
+                        10.0, (-0.4 * (_mag_vals[0] + _mag_vals[1] + 48.60))
+                    )
+                    _flux1_nu *= u.erg / (u.cm * u.cm * u.s * u.Hz)
+                    _flux1 = _flux1_nu.to(
+                        fluxunit,
+                        equivalencies=u.spectral_density(poss_bands[pband_name][1] * u.micron),
+                    )
+                    _flux2_nu = np.power(
+                        10.0, (-0.4 * (_mag_vals[0] - _mag_vals[1] + 48.60))
+                    )
+                    _flux2_nu *= u.erg / (u.cm * u.cm * u.s * u.Hz)
+                    _flux2 = _flux2_nu.to(
+                        fluxunit,
+                        equivalencies=u.spectral_density(poss_bands[pband_name][1] * u.micron),
+                    )
+                    self.band_fluxes[pband_name] = (
+                        0.5 * (_flux1.value + _flux2.value),
+                        0.5 * (_flux2.value - _flux1.value),
+                    )
+                    self.band_waves[pband_name] = poss_bands[pband_name][1]
                 elif _mag_vals[2] == "mJy":
                     self.band_waves[pband_name] = poss_bands[pband_name][1]
                     mfac = (
@@ -821,9 +869,10 @@
             if len(indxs) > 0:
                 self.npts[indxs] = 0
 
-        # add units
-        self.fluxes = self.fluxes.value * (u.Jy)
-        self.uncs = self.uncs.value * (u.Jy)
+        self.fluxes = self.fluxes.to(
+            fluxunit, equivalencies=u.spectral_density(self.waves)
+        )
+        self.uncs = self.uncs.to(fluxunit, equivalencies=u.spectral_density(self.waves))
 
     def read_nircam_ss(self, line, path="./"):
         """

measure_extinction/utils/fit_model.py

@@ -70,6 +70,7 @@
         fits the model.
 
         Parameters
+        ``
         ----------
         params : floats
             parameters of the model
@@ -99,10 +100,12 @@
             gvals = (self.weights[cspec] > 0) & (np.isfinite(hi_ext_modsed[cspec]))
             chiarr = np.square(
                 (
-                    obsdata.data[cspec].fluxes[gvals].value
-                    - (hi_ext_modsed[cspec][gvals] * (norm_data / norm_model))
+                    (
+                        obsdata.data[cspec].fluxes[gvals].value
+                        - (hi_ext_modsed[cspec][gvals] * (norm_data / norm_model))
+                    )
+                    * self.weights[cspec][gvals]
                 )
-                * self.weights[cspec][gvals]
             )
             lnl += -0.5 * np.sum(chiarr)
 
@@ -238,14 +241,14 @@
             (indxs,) = np.where(sampler.lnprobability[k] == tmax_lnp)
             fit_params_best = sampler.chain[k, indxs[0], :]
 
-    ndim = len(fit_params_best)
-    params_best = np.zeros((ndim + 3))
-    params_best[0:ndim] = fit_params_best
-    params_best[ndim] = params_best[3] / params_best[4]
-    params_best[ndim + 1] = (10 ** params_best[10]) / params_best[3]
-    params_best[ndim + 2] = (10 ** params_best[10]) / params_best[ndim]
+    # ndim = len(fit_params_best)
+    # params_best = np.zeros((ndim + 3))
+    # params_best[0:ndim] = fit_params_best
+    # params_best[ndim] = params_best[3] / params_best[4]
+    # params_best[ndim + 1] = (10 ** params_best[10]) / params_best[3]
+    # params_best[ndim + 2] = (10 ** params_best[10]) / params_best[ndim]
 
-    return params_best
+    return fit_params_best
 
 
 def get_percentile_params(samples):

measure_extinction/utils/make_all_tlusty_obsdata.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 
 import glob
+import argparse
 
 from measure_extinction.utils.make_obsdata_from_model import make_obsdata_from_model
 
@@ -61,20 +62,61 @@
     return model_params
 
 
+def decode_params_wd(filename):
+    """
+    Decode the tlusty filenames for the model parameters
+    """
+    model_params = {}
+
+    slashpos = filename.rfind("/")
+    periodpos = filename.rfind(".spec")
+
+    tpos = filename.find("t", slashpos)
+    gpos = filename.find("g", slashpos)
+
+    model_params["Teff"] = float(filename[tpos + 1 : gpos])
+    model_params["logg"] = float(filename[gpos + 1 : periodpos - 1]) * 0.01
+    model_params["vturb"] = 0.0
+    model_params["Z"] = 1.0   # ratio to solar
+
+    if model_params["Teff"] < 10000.0:
+        model_params["Teff"] *= 100.0
+
+    return model_params
+
+
 if __name__ == "__main__":
-    tlusty_models = glob.glob(
-        "/home/kgordon/Python/extstar_data/Models/Tlusty_2023/*v10.spec.gz"
+
+    # commandline parser
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "--grid",
+        choices=["tlusty", "wd_hubeny"],
+        default="tlusty",
+        help="Grid to use",
     )
+    args = parser.parse_args()
+
+    if args.grid == "wd_hubeny":
+        mfilestr = "/home/kgordon/Python/extstar_data/Models/WD_Hubeny/*.spec"
+        decodefunc = decode_params_wd
+        outbase = "wd_hubeny"
+    else:
+        mfilestr = "/home/kgordon/Python/extstar_data/Models/Tlusty_2023/*v10.spec.gz"
+        decodefunc = decode_params
+        outbase = "tlusty"
+
+    tlusty_models = glob.glob(mfilestr)
 
     for cfname in tlusty_models:
         # parse the filename to get the model parameters
-        model_params = decode_params(cfname)
+        model_params = decodefunc(cfname)
 
         # get the base filename for the output files
         slashpos = cfname.rfind("/")
         periodpos = cfname.rfind(".spec")
 
-        basename = "tlusty_{}".format(cfname[slashpos + 1 : periodpos])
+        basename = f"{outbase}_{cfname[slashpos + 1 : periodpos]}"
 
         print(cfname)
         print(basename)

measure_extinction/utils/make_obsdata_from_model.py

@@ -399,6 +399,8 @@ def make_obsdata_from_model(
         "HST_WFC3_UVIS1_F275W",
         "HST_WFC3_UVIS1_F336W",
         "HST_WFC3_UVIS1_F475W",
+        "HST_WFC3_UVIS1_F625W",
+        "HST_WFC3_UVIS1_F775W",
         "HST_WFC3_UVIS1_F814W",
         "HST_WFC3_IR_F110W",
         "HST_WFC3_IR_F160W",

measure_extinction/utils/merge_stis_spec.py

@@ -56,6 +56,7 @@
 
     if args.ralph:
         sfilename = "%s/%s/%s.mrg" % (args.inpath, args.waveregion, args.starname)
+        sfilename = f"{args.inpath}{args.starname}.mrg"
 
         # determine the line for the 1st data (can vary between files)
         f = open(sfilename, "r")