Update notebooks to generate HTML build

Author: haticekaratay

notebooks/MIRI_IFU_YSOs_in_the_LMC/isha_nayak_ysos_in_the_lmc.ipynb

@@ -622,7 +622,7 @@
     "\n",
     "# Assign to variable to make it more readable for line below\n",
     "spec_contsub_1 = spec[count_axis:len(spec.spectral_axis)] - y_continuum_1[count_axis:len(spec.spectral_axis)]\n",
-    "spec_contsub_2 = spec[0:count_axis] - y_continuum_2[0:count_axis]\n"
+    "spec_contsub_2 = spec[0:count_axis] - y_continuum_2[0:count_axis]"
    ]
   },
   {
@@ -1157,13 +1157,6 @@
     "plt.show()\n",
     "plt.close()"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -1182,7 +1175,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.9.13"
   }
  },
  "nbformat": 4,

notebooks/MRS_Mstar_analysis/JWST_Mstar_dataAnalysis_analysis.ipynb

@@ -97,31 +97,21 @@
     "# Import astropy packages \n",
     "from astropy import units as u\n",
     "from astropy.io import ascii\n",
-    "from astropy.wcs import WCS\n",
-    "from astropy.table import Table, vstack\n",
-    "from astropy.stats import sigma_clipped_stats\n",
     "from astropy.nddata import StdDevUncertainty\n",
-    "from astropy.io import fits # added by BAS on 8 April 2021\n",
-    "from astropy.utils.data import get_pkg_data_filename\n",
     "from astropy.utils.data import download_file\n",
     "\n",
     "# To find stars in the MRS spectralcubes and do aperture photometry\n",
-    "from photutils.aperture import CircularAperture\n",
     "from photutils.detection import DAOStarFinder\n",
     "\n",
     "# To deal with 1D spectrum\n",
     "from specutils import Spectrum1D\n",
-    "from specutils.fitting import fit_generic_continuum\n",
-    "from specutils.manipulation import box_smooth, extract_region, SplineInterpolatedResampler\n",
+    "from specutils.manipulation import box_smooth, extract_region\n",
     "from specutils.analysis import line_flux, centroid, equivalent_width\n",
     "from specutils.spectra import SpectralRegion\n",
     "from specutils import SpectrumList\n",
     "from jdaviz import Specviz\n",
     "from jdaviz import Cubeviz\n",
     "\n",
-    "# To fit a curve to the data\n",
-    "from scipy.optimize import curve_fit\n",
-    "\n",
     "# Display the video\n",
     "from IPython.display import HTML, YouTubeVideo"
    ]
@@ -157,10 +147,10 @@
     "    if key in dict.keys():\n",
     "        print(\"Present, \", end=\" \")\n",
     "        print(\"value =\", dict[key])\n",
-    "        return(True)\n",
+    "        return True\n",
     "    else:\n",
     "        print(\"Not present\")\n",
-    "        return(False)"
+    "        return False"
    ]
   },
   {
@@ -240,7 +230,7 @@
     "fnuall = fnuallarr[srtind]\n",
     "\n",
     "# Developer Note: We put in errors of 0.0001, but uncertainties need to be fixed\n",
-    "dfnuall = (0.0001)*np.ones(len(fnuall))\n"
+    "dfnuall = (0.0001)*np.ones(len(fnuall))"
    ]
   },
   {
@@ -856,7 +846,7 @@
     "\n",
     "plt.xlabel('Wavelength (microns)')\n",
     "plt.ylabel(\"Flux ({:latex})\".format(spec.flux.unit))\n",
-    "plt.title(\"10$\\mu$m feature plus local continuum\")\n",
+    "plt.title(r\"10$\\mu$m feature plus local continuum\")\n",
     "plt.legend(frameon=False, fontsize='medium')\n",
     "plt.tight_layout()\n",
     "plt.show()\n",
@@ -872,7 +862,7 @@
     "\n",
     "plt.xlabel('Wavelength (microns)')\n",
     "plt.ylabel(\"Flux ({:latex})\".format(spec.flux.unit))\n",
-    "plt.title(\"Continuum subtracted 10$\\mu$m feature\")\n",
+    "plt.title(r\"Continuum subtracted 10$\\mu$m feature\")\n",
     "plt.tight_layout()\n",
     "plt.show()\n",
     "plt.close()"
@@ -953,8 +943,7 @@
     "\n",
     "tau = -(np.log(line_spec.flux.value / line_y_continuum.value))\n",
     "optdepth_spec = Spectrum1D(spectral_axis=line_spec.spectral_axis,\n",
-    "                           flux=tau*(u.Jy/u.Jy))\n",
-    "        "
+    "                           flux=tau*(u.Jy/u.Jy))"
    ]
   },
   {
@@ -1044,7 +1033,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.9.13"
   }
  },
  "nbformat": 4,