Added another tutorial, "synphot-model-spec"

tutorials/notebooks/synphot-measured-spec/synphot-measured-spec.ipynb

@@ -42,7 +42,7 @@
    "metadata": {},
    "source": [
     "## Summary\n",
-    "<a href=\"https://synphot.readthedocs.io/en/latest/index.html\">`synphot`</a> is an astropy-affiliated package for creating synthetic photometry in Python. In this tutorial we will show how to use `synphot` to predict the photometric fluxes of a galaxy observed by SDSS. In particular, we will:\n",
+    "<a href=\"https://synphot.readthedocs.io/en/latest/index.html\"><tt>synphot</tt></a> is an astropy-affiliated package for creating synthetic photometry in Python. In this tutorial we will show how to use <tt>synphot</tt> to predict the photometric fluxes of a galaxy observed by SDSS. In particular, we will:\n",
     "<ol>\n",
     "<li><a href=\"#sdss\">Get the observed spectrum of our target from SDSS</a></li>\n",
     "<li><a href=\"#source_spectrum\">Construct a source spectrum object</a></li>\n",
@@ -54,7 +54,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 47,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -93,12 +93,12 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "To download the spectrum, first set the coordinates for the object using <a href=\"https://docs.astropy.org/en/stable/api/astropy.coordinates.SkyCoord.html\" target=\"_blank\">`astropy.coordinates.SkyCoord`</a>:"
+    "To download the spectrum, first set the coordinates for the object using <a href=\"https://docs.astropy.org/en/stable/api/astropy.coordinates.SkyCoord.html\" target=\"_blank\"><tt>astropy.coordinates.SkyCoord</tt></a>:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 31,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -111,23 +111,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Then use these coordinates with <a href=\"https://astroquery.readthedocs.io/en/latest/sdss/sdss.html\">`astroquery.sdss`</a> to get a .fits file of the spectrum observed by SDSS:"
+    "Then use these coordinates with <a href=\"https://astroquery.readthedocs.io/en/latest/sdss/sdss.html\"><tt>astroquery.sdss</tt></a> to get a .fits file of the spectrum observed by SDSS:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": 18,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/tiffanyjansen/anaconda3/lib/python3.7/site-packages/astroquery/sdss/core.py:856: VisibleDeprecationWarning: Reading unicode strings without specifying the encoding argument is deprecated. Set the encoding, use None for the system default.\n",
-      "  comments='#'))\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "spectrum_fits = SDSS.get_spectra(coordinates=coords)\n",
     "data = spectrum_fits[0][1].data"
@@ -142,7 +133,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": 19,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -162,12 +153,12 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "To do synthetic photometry with `synphot`, you must first make an object out of your target's spectrum with <a href=\"https://synphot.readthedocs.io/en/latest/synphot/spectrum.html#arrays\">`synphot.spectrum.SourceSpectrum`</a>. Since we are constructing the source spectrum from arrays of data, we specify that the model type is Empirical1D and pass in the arrays (e.g. <code>points=wavelengths</code> and <code>lookup_table=flux</code>):"
+    "To do synthetic photometry with <tt>synphot</tt>, you must first make an object out of your target's spectrum with <a href=\"https://synphot.readthedocs.io/en/latest/synphot/spectrum.html#arrays\"><tt>synphot.spectrum.SourceSpectrum</tt></a>. Since we are constructing the source spectrum from arrays of data, we specify that the model type is Empirical1D and pass in the arrays (e.g. <code>points=wavelengths</code> and <code>lookup_table=flux</code>):"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": 20,
    "metadata": {},
    "outputs": [
     {
@@ -202,26 +193,26 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Next we want to model the effect of observing this object through the SDSS bandpasses. Similar to how we made the spectral data into a synphot object, we will also need to construct bandpass objects so that the two can be easily convolved using `synphot`."
+    "Next we want to model the effect of observing this object through the SDSS bandpasses. Similar to how we made the spectral data into a synphot object, we will also need to construct bandpass objects so that the two can be easily convolved using <tt>synphot</tt>."
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "To obtain the filter transmission functions of the SDSS bandpasses, we use <a href=\"https://docs.astropy.org/en/stable/api/astropy.utils.data.download_file.html\" target=\"_blank\">`astropy.utils.data.download_file`</a> to download the transmission file from the <a href=\"http://svo2.cab.inta-csic.es/theory/fps/index.php?mode=voservice\">Spanish Virtual Observatory</a> filter database. These transmission functions include the effect of the CCD's quantum efficiency on the spectrum."
+    "To obtain the filter transmission functions of the SDSS bandpasses, we use <a href=\"https://docs.astropy.org/en/stable/api/astropy.utils.data.download_file.html\" target=\"_blank\"><tt>astropy.utils.data.download_file</tt></a> to download the transmission file from the <a href=\"http://svo2.cab.inta-csic.es/theory/fps/index.php?mode=voservice\">Spanish Virtual Observatory</a> filter database. These transmission functions include the effect of the CCD's quantum efficiency on the spectrum."
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "To construct a bandpass from a file, use `synphot.spectrum`'s <a href=\"https://synphot.readthedocs.io/en/latest/synphot/spectrum.html\">SpectralElement</a> with its <a href=\"https://synphot.readthedocs.io/en/latest/api/synphot.spectrum.SourceSpectrum.html#synphot.spectrum.SourceSpectrum.from_file\" target=\"_blank\">from_file</a> method:"
+    "To construct a bandpass from a file, use <tt>synphot.spectrum</tt>'s <a href=\"https://synphot.readthedocs.io/en/latest/synphot/spectrum.html\"><tt>SpectralElement</tt></a> with its <a href=\"https://synphot.readthedocs.io/en/latest/api/synphot.spectrum.SourceSpectrum.html#synphot.spectrum.SourceSpectrum.from_file\" target=\"_blank\"><tt>from_file</tt></a> method:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 35,
+   "execution_count": 21,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -249,7 +240,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 36,
+   "execution_count": 22,
    "metadata": {},
    "outputs": [
     {
@@ -258,7 +249,7 @@
        "(0, 0.5)"
       ]
      },
-     "execution_count": 36,
+     "execution_count": 22,
      "metadata": {},
      "output_type": "execute_result"
     },
@@ -303,12 +294,12 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We can then model the observation by convolving the object's spectrum with the filter transmission functions using <a href=\"https://synphot.readthedocs.io/en/latest/synphot/observation.html\">`synphot.observation`</a>:"
+    "We can then model the observation by convolving the object's spectrum with the filter transmission functions using <a href=\"https://synphot.readthedocs.io/en/latest/synphot/observation.html\"><tt>synphot.observation</tt></a>:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 37,
+   "execution_count": 23,
    "metadata": {},
    "outputs": [
     {
@@ -329,12 +320,12 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We can then use the `synphot.observation` method <a href=\"https://synphot.readthedocs.io/en/latest/api/synphot.observation.Observation.html?highlight=effstim#synphot.observation.Observation.effstim\" target=\"_blank\">`effstim`</a> to calculate the total flux obtained in each band. In order to compare our synthetic fluxes to those measured by SDSS, we need to convert the flux to units compatable with SDSS data. <a href=\"http://www.sdss3.org/dr8/algorithms/magnitudes.php#nmgy\" target=\"_blank\">SDSS uses nanomaggies as a flux unit</a>, which we can convert to with the `astropy.units` methods <a href=\"https://docs.astropy.org/en/stable/api/astropy.units.quantity.Quantity.html#astropy.units.quantity.Quantity.to\" target=\"_blank\">`to`</a> and <a href=\"https://docs.astropy.org/en/stable/api/astropy.units.photometric.zero_point_flux.html?highlight=zero%20point%20flux\" target=\"_blank\">`zero_point_flux`</a> given the zero point of this magnitude scale (3631.1 Jy):"
+    "We can then use the <tt>synphot.observation</tt> method <a href=\"https://synphot.readthedocs.io/en/latest/api/synphot.observation.Observation.html?highlight=effstim#synphot.observation.Observation.effstim\" target=\"_blank\"><tt>effstim</tt></a> to calculate the total flux obtained in each band. In order to compare our synthetic fluxes to those measured by SDSS, we need to convert the flux to units compatable with SDSS data. <a href=\"http://www.sdss3.org/dr8/algorithms/magnitudes.php#nmgy\" target=\"_blank\">SDSS uses nanomaggies as a flux unit</a>, which we can convert to with the <tt>astropy.units</tt> methods <a href=\"https://docs.astropy.org/en/stable/api/astropy.units.quantity.Quantity.html#astropy.units.quantity.Quantity.to\" target=\"_blank\"><tt>to</tt></a> and <a href=\"https://docs.astropy.org/en/stable/api/astropy.units.photometric.zero_point_flux.html?highlight=zero%20point%20flux\" target=\"_blank\"><tt>zero_point_flux</tt></a> given the zero point of this magnitude scale (3631.1 Jy):"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 38,
+   "execution_count": 24,
    "metadata": {},
    "outputs": [
     {
@@ -362,19 +353,19 @@
    "metadata": {},
    "source": [
     "<a id=\"compare\"></a>\n",
-    "### 5. How well does `synphot` do?"
+    "### 5. How well does <tt>synphot</tt> do?"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "To compare the g,r,i empirical fluxes to what we predict with `synphot`, we first get the fluxes measured by the SDSS fibers by using <a href=\"https://astroquery.readthedocs.io/en/latest/api/astroquery.sdss.SDSSClass.html#astroquery.sdss.SDSSClass.query_crossid\">`astroquery.sdss.query_crossid`</a> and setting the photoObj to \"fiberFlux_band\". For a full list of photoObj fields, <a href=\"https://skyserver.sdss.org/dr12/en/help/browser/browser.aspx?cmd=description+PhotoObj+V#&&history=description+PhotoObj+V\">see here</a>."
+    "To compare the g,r,i empirical fluxes to what we predict with <tt>synphot</tt>, we first get the fluxes measured by the SDSS fibers by using <a href=\"https://astroquery.readthedocs.io/en/latest/api/astroquery.sdss.SDSSClass.html#astroquery.sdss.SDSSClass.query_crossid\"><tt>astroquery.sdss.query_crossid</tt></a> and setting the photoObj to \"fiberFlux_band\". For a full list of photoObj fields, <a href=\"https://skyserver.sdss.org/dr12/en/help/browser/browser.aspx?cmd=description+PhotoObj+V#&&history=description+PhotoObj+V\">see here</a>."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 39,
+   "execution_count": 25,
    "metadata": {},
    "outputs": [
     {
@@ -397,7 +388,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 40,
+   "execution_count": 26,
    "metadata": {},
    "outputs": [
     {
@@ -408,7 +399,7 @@
        " 'i': <Quantity [294.157] nmgy>}"
       ]
      },
-     "execution_count": 40,
+     "execution_count": 26,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -421,21 +412,21 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Compare the `synphot` fluxes to the observed fluxes by plotting on a 1-1 line:"
+    "Compare the <tt>synphot</tt> fluxes to the observed fluxes by plotting on a 1-1 line:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 41,
+   "execution_count": 27,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0xb21695320>"
+       "<matplotlib.legend.Legend at 0xb1afaad30>"
       ]
      },
-     "execution_count": 41,
+     "execution_count": 27,
      "metadata": {},
      "output_type": "execute_result"
     },

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