adding in NIRCam

measure_extinction/extdata.py

@@ -27,6 +27,7 @@
     "SpeX_SXD",
     "SpeX_LXD",
     "IRS",
+    "NIRCam_SS",
     "MIRI_IFU",
 ]
 
@@ -262,7 +263,7 @@ class ExtData:
     """
     Extinction for a single line-of-sight
 
-    Atributes:
+    Attributes:
 
     type : string
         extinction curve type (e.g., elx or alax)

measure_extinction/stardata.py

@@ -825,6 +825,30 @@ def read_irs(self, line, path="./", use_corfac=True, corfac=None):
         self.fluxes = self.fluxes.value * (u.Jy)
         self.uncs = self.uncs.value * (u.Jy)
 
+    def read_nircam_ss(self, line, path="./"):
+        """
+        Read in Webb/NIRCam slitless spectra
+
+        Parameters
+        ----------
+        line : string
+            formatted line from DAT file
+            example: 'NIRCam_SS = hd029647_irs.fits'
+
+        path : string, optional
+            location of the FITS files path
+
+        Returns
+        -------
+        Updates self.(file, wave_range, waves, flux, uncs, npts, n_waves)
+        """
+        self.read_spectra(line, path)
+
+        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_miri_ifu(self, line, path="./"):
         """
         Read in Webb/MRS IFU spectra
@@ -833,7 +857,7 @@ def read_miri_ifu(self, line, path="./"):
         ----------
         line : string
             formatted line from DAT file
-            example: 'IRS = hd029647_irs.fits'
+            example: 'MIRI_IFU = hd029647_irs.fits'
 
         path : string, optional
             location of the FITS files path
@@ -1106,6 +1130,16 @@ def read(self, deredden=False, only_bands=None):
                         )
                     else:
                         warnings.warn(f"{fname} does not exist", UserWarning)
+                elif line.find("NIRCam_SS") == 0:
+                    fname = _getspecfilename(line, self.path)
+                    if os.path.isfile(fname):
+                        self.data["NIRCam_SS"] = SpecData("NIRCam_SS")
+                        self.data["NIRCam_SS"].read_miri_ifu(
+                            line,
+                            path=self.path,
+                        )
+                    else:
+                        warnings.warn(f"{fname} does not exist", UserWarning)
                 elif line.find("MIRI_IFU") == 0:
                     fname = _getspecfilename(line, self.path)
                     if os.path.isfile(fname):

measure_extinction/utils/merge_miri_ifu_spec.py

@@ -37,14 +37,10 @@
     args = parser.parse_args()
 
     sfilename = f"{args.inpath}{args.starname}*order*.fits"
-    print(sfilename)
     sfiles = glob.glob(sfilename)
-    print(sfiles)
     stable = []
     for cfile in sfiles:
-        print(cfile)
         cdata = QTable.read(cfile)
-        print(cdata.colnames)
         cdata.rename_column("wavelength", "WAVELENGTH")
         cdata.rename_column("flux", "FLUX")
         cdata.rename_column("unc", "ERROR")
@@ -104,6 +100,9 @@
     ax.set_xlabel(r"$\lambda$ [$\AA$]")
     ax.set_ylabel(r"F($\lambda$)")
 
+    ax.set_xscale("log")
+    ax.set_yscale("log")
+
     ax.legend()
     fig.tight_layout()
 

measure_extinction/utils/merge_nircam_spec.py

@@ -0,0 +1,115 @@
+#!/usr/bin/env python
+
+import glob
+import argparse
+import numpy as np
+import pkg_resources
+import matplotlib.pyplot as plt
+
+from astropy.table import QTable
+import astropy.units as u
+
+from measure_extinction.merge_obsspec import merge_nircam_ss_obsspec
+
+
+fluxunit = u.erg / (u.cm * u.cm * u.s * u.angstrom)
+
+
+if __name__ == "__main__":
+
+    # commandline parser
+    parser = argparse.ArgumentParser()
+    parser.add_argument("starname", help="name of star (filebase)")
+    parser.add_argument(
+        "--inpath",
+        help="path where original data files are stored",
+        default=pkg_resources.resource_filename("measure_extinction", "data/Orig"),
+    )
+    parser.add_argument(
+        "--outpath",
+        help="path where merged spectra will be stored",
+        default=pkg_resources.resource_filename("measure_extinction", "data/Out"),
+    )
+    parser.add_argument("--outname", help="Output filebase")
+    parser.add_argument("--png", help="save figure as a png file", action="store_true")
+    parser.add_argument("--eps", help="save figure as an eps file", action="store_true")
+    parser.add_argument("--pdf", help="save figure as a pdf file", action="store_true")
+    args = parser.parse_args()
+
+    sfilename = f"{args.inpath}{args.starname}*order*.fits"
+    sfiles = glob.glob(sfilename)
+    stable = []
+    for cfile in sfiles:
+        cdata = QTable.read(cfile)
+        cdata.rename_column("wavelength", "WAVELENGTH")
+        cdata.rename_column("flux", "FLUX")
+        cdata.rename_column("unc", "ERROR")
+        cdata["WAVELENGTH"] *= u.micron
+        cdata["NPTS"] = np.full((len(cdata["FLUX"])), 1.0)
+        cdata["NPTS"][cdata["FLUX"] == 0.0] = 0.0
+        stable.append(cdata)
+
+    rb_mrs = merge_nircam_ss_obsspec(stable)
+    if args.outname:
+        outname = args.outname
+    else:
+        outname = args.starname.lower()
+    mrs_file = f"{outname}_nircam_ss.fits"
+    rb_mrs.write(f"{args.outpath}/{mrs_file}", overwrite=True)
+
+    # plot the original and merged Spectra
+    fontsize = 14
+    font = {"size": fontsize}
+    plt.rc("font", **font)
+    plt.rc("lines", linewidth=2)
+    plt.rc("axes", linewidth=2)
+    plt.rc("xtick.major", width=2)
+    plt.rc("ytick.major", width=2)
+
+    fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(10, 5.5))
+
+    for ctable in stable:
+        gvals = ctable["NPTS"] > 0
+        cfluxes = (
+            ctable["FLUX"]
+            .to(fluxunit, equivalencies=u.spectral_density(ctable["WAVELENGTH"]))
+            .value
+        )
+        ax.plot(
+            ctable["WAVELENGTH"][gvals],
+            cfluxes[gvals],
+            "k-",
+            alpha=0.5,
+            label="orig",
+        )
+    gvals = rb_mrs["NPTS"] > 0
+    cfluxes = (
+        rb_mrs["FLUX"]
+        .to(fluxunit, equivalencies=u.spectral_density(ctable["WAVELENGTH"]))
+        .value
+    )
+
+    ax.plot(
+        rb_mrs["WAVELENGTH"][gvals].to(u.micron),
+        rb_mrs["FLUX"][gvals],
+        "b-",
+        alpha=0.5,
+        label="merged",
+    )
+
+    ax.set_xlabel(r"$\lambda$ [$\AA$]")
+    ax.set_ylabel(r"F($\lambda$)")
+
+    ax.set_xscale("log")
+    ax.set_yscale("log")
+
+    ax.legend()
+    fig.tight_layout()
+
+    fname = mrs_file.replace(".fits", "")
+    if args.png:
+        fig.savefig(f"{fname}.png")
+    elif args.pdf:
+        fig.savefig(f"{fname}.pdf")
+    else:
+        plt.show()