Merge branch 'BEAST-Fitting:master' into master

.github/workflows/tox-tests.yml

@@ -95,14 +95,14 @@ jobs:
  - name: Set up python for coverage test
  uses: actions/setup-python@v4
  with:
- python-version: 3.12
+ python-version: 3.9
  - name: Install base dependencies
  run: |
  python -m pip install --upgrade pip
  python -m pip install tox
  - name: Test with tox
  run: |
- tox -e py312-cov -- --remote-data
+ tox -e py309-cov -- --remote-data
  - name: Upload coverage to codecov
  uses: codecov/codecov-action@v1
  with:

README.rst

@@ -4,7 +4,7 @@ BEAST
 The Bayesian Extinction and Stellar Tool (BEAST) fits the ultraviolet to
 near-infrared photometric SEDs of stars to extract stellar and
 dust extinction parameters.
-The stellar parameters are age (t), mass (M), metallicity (M), and distance (d).
+The stellar parameters are age (t), mass (M), metallicity (Z), and distance (d).
 The dust extinction parameters are dust column (Av), average grain size (Rv),
 and mixing between type A and B extinction curves (fA).
 

beast/observationmodel/tests/test_filters_and_vega_consistent.py

@@ -0,0 +1,33 @@
+from astropy.table import QTable
+
+from beast.config import __ROOT__
+from beast.tools import get_libfiles
+
+
+def test_filters_and_vega_consistent():
+ """
+ Test to ensure that the filters.hd5 and vega.hd5 are consistent.
+ In other words, both have the same filters.
+ """
+
+ # download the BEAST library files
+ get_libfiles.get_libfiles(vega_filters_only=True)
+
+ ftab = QTable.read(__ROOT__ + "filters.hd5", path="content")
+ vtab = QTable.read(__ROOT__ + "vega.hd5", path="sed")
+
+ otxt = ""
+ for cfilt in ftab["TABLENAME"].data:
+ if cfilt not in vtab["FNAME"].data:
+ otxt = f"{otxt} {cfilt}"
+ assert otxt == "", "filters in filters.hd5 missing from vega.hd5:" + otxt
+
+ otxt = ""
+ for cfilt in vtab["FNAME"].data:
+ if cfilt not in ftab["TABLENAME"].data:
+ otxt = f"{otxt} {cfilt}"
+ assert otxt == "", "filters in vega.hd5 missing from filters.hd5:" + otxt
+
+
+if __name__ == "__main__": # pragma: no cover
+ test_filters_and_vega_consistent()

beast/plotting/plot_filters.py

@@ -15,12 +15,10 @@
 def plot_filters(
  filter_names,
  filterLib=None,
- save_name="beast_filters",
- xlim=[1.4e3, 2e4],
+ xlim=None,
  ylim=[1e-4, 2],
  show_plot=True,
 ):
-
  """Plots transmission curves in log-log space.
 
  Parameters
@@ -42,32 +40,47 @@ def plot_filters(
  fig, ax = plt.subplots(1, 1, figsize=(10, 6))
 
  # wavelength grid in angstroms for response functions
- waves = np.logspace(3, np.log10(3e4), 501)
+ # cover all HST and JWST wavelengths
+ waves = np.logspace(np.log10(912.0), np.log10(3e5), 1001)
 
  # read in the filter response functions
  flist = phot.load_filters(
  filter_names, interp=True, lamb=waves, filterLib=filterLib
  )
 
  color_indices = np.log10(np.array(np.sort([f.norm for f in flist])))
- color_indices -= color_indices.min()
- color_indices /= color_indices.max()
+ if len(color_indices) > 1:
+ color_indices -= color_indices.min()
+ color_indices /= color_indices.max()
+ else:
+ color_indices = [0.0]
 
  cmap = mpl.cm.plasma
  # ax.set_prop_cycle(color=[cmap(i) for i in color_indices])
  color = iter(cmap(np.linspace(0.2, 0.8, len(filter_names))))
 
+ dxlim = np.array([3e5, 912.0]) * 1e-4
  for f in flist:
+ wavelength = f.wavelength * 1e-4
  c = next(color)
- ax.plot(f.wavelength, f.transmit, color=c, lw=2)
- ax.fill_between(f.wavelength, f.transmit, alpha=0.2, color=c)
+ ax.plot(wavelength, f.transmit, color=c, lw=2)
+ ax.fill_between(wavelength, f.transmit, alpha=0.2, color=c)
+ yval_text = max(f.transmit * 0.1)
  ax.text(
- np.nanmean(f.wavelength[f.transmit > 100.0 * ylim[0]]),
- 1.3 * np.nanmax(f.transmit[f.transmit > ylim[0]]),
+ np.nanmean(wavelength[f.transmit > yval_text]),
+ 1.3 * np.nanmax(f.transmit[f.transmit > yval_text]),
  f.name.split("_")[-1],
  ha="center",
  color=c,
  )
+ gvals = (f.transmit > ylim[0]) & (f.transmit < ylim[1])
+ if min(wavelength[gvals]) < dxlim[0]:
+ dxlim[0] = min(wavelength[gvals])
+ if max(wavelength[gvals]) > dxlim[1]:
+ dxlim[1] = max(wavelength[gvals])
+
+ if xlim is None:
+ xlim = dxlim
 
  ax.set_xscale("log")
  ax.set_yscale("log")
@@ -77,7 +90,7 @@ def plot_filters(
  ax.set_ylabel(r"$B_i(\lambda)$")
 
  # ax.set_xticks([0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 2.0])
- ax.get_xaxis().set_major_formatter(mpl.ticker.ScalarFormatter())
+ # ax.get_xaxis().set_major_formatter(mpl.ticker.ScalarFormatter())
 
  fig.tight_layout()
 
@@ -95,9 +108,7 @@ def plot_filters(
  default="filters.appendVegaFilter",
  help="Save figure to file",
  )
- args = parser.parse_args()
-
- filter_names = [
+ def_filter_names = [
  "HST_WFC3_F225W",
  "HST_WFC3_F275W",
  "HST_WFC3_F336W",
@@ -107,8 +118,12 @@ def plot_filters(
  "HST_WFC3_F110W",
  "HST_WFC3_F160W",
  ]
+ parser.add_argument(
+ "filter_names", help="names of filters", nargs="+", default=def_filter_names
+ )
+ args = parser.parse_args()
 
- fig = plot_filters(filter_names, show_plot=False)
+ fig = plot_filters(args.filter_names, show_plot=False)
 
  if args.tex:
  plt.rc({"usetex": True})

beast/tests/test_regresscheck.py

@@ -68,7 +68,7 @@ def setUpClass(cls):
 
  cls.dset = "metal"
  if cls.dset == "metal":
- cls.basesubdir = "metal_small_9Nov22/"
+ cls.basesubdir = "metal_small/"
  cls.basename = f"{cls.basesubdir}beast_metal_small"
  cls.obsname = f"{cls.basesubdir}14675_LMC-13361nw-11112.gst_samp.fits"
  cls.astname = f"{cls.basesubdir}14675_LMC-13361nw-11112.gst.fake.fits"

beast/tools/get_libfiles.py

@@ -15,12 +15,13 @@ def _download_rename(filename, url_loc, local_loc):
  return filename
 
 
-def get_libfiles():
+def get_libfiles(vega_filters_only=False):
  """
  Download all the library files needed by the BEAST
  """
  for ckey, clib in libs.items():
- _download_rename(clib, libs_server, __ROOT__)
+ if ((not vega_filters_only) or (vega_filters_only & (ckey in ["vega", "filters"]))):
+ _download_rename(clib, libs_server, __ROOT__)
 
 
 if __name__ == "__main__": # pragma: no cover