updates to examples and documentation

README.md

@@ -34,8 +34,9 @@ outlines the corrections and component calculation pipeline
 
 3. [RV Calculations](https://github.com/tamarervin/sdo_hmi_rvs/blob/main/sdo_hmi_rvs/examples/rv_calculation.ipynb):
 outlines calculation of full model RV from velocity components  
-   * requires input CSV with velocity components from [example 2](https://github.com/tamarervin/sdo_hmi_rvs/blob/main/sdo_hmi_rvs/examples/component_calculations.ipynb)
-
+   * requires input CSV with velocity components from [example 2](https://github.com/tamarervin/sdo_hmi_rvs/blob/main/sdo_hmi_rvs/examples/component_calculations.ipynb)  
+   * an example CSV file with calculations is stored [here](https://github.com/tamarervin/sdo_hmi_rvs/blob/main/sdo_hmi_rvs/products/csv_files/calcs/example_calcs.csv)
+
 4. [Full Pipeline](https://github.com/tamarervin/sdo_hmi_rvs/blob/main/sdo_hmi_rvs/examples/full_pipeline.ipynb):
 full end-to-end pipeline to calculate 'sun-as-a-star' RVs and magnetic observables 
 

mkdocs/docs/examples/docs_rv_calcs.ipynb

@@ -7,7 +7,11 @@
     "\n",
     "1. **calculate solar velocities:** calculate solar velocities and save to csv\n",
     "2. **get component lists:** using pandas to get the lists of each relevant component\n",
-    "3. **calculate RVs and save to csv:**  calculate RVs using optimized parameters"
+    "3. **calculate RVs and save to csv:**  calculate RVs using optimized parameters\n",
+    "\n",
+    "\n",
+    "**NOTE:** this is purely an example but requires ground-based Solar RV\n",
+    "measurements for fitting"
    ],
    "metadata": {
     "collapsed": false

mkdocs/docs/examples/docs_solar_corrections.ipynb

@@ -482,7 +482,8 @@
    "execution_count": null,
    "outputs": [],
    "source": [
-    "map_int_cor = [sfuncs.corrected_map(Iflat[i], hmi_int[i], map_type='Corrected-Intensitygram', frame=frames.HeliographicCarrington) for i in range(0, len(hmi_int))]"
+    "map_int_cor = [sfuncs.corrected_map(Iflat[i], hmi_int[i], map_type='Corrected-Intensitygram',\n",
+    "                                    frame=frames.HeliographicCarrington) for i in range(0, len(hmi_int))]"
    ],
    "metadata": {
     "collapsed": false,

mkdocs/site/examples/docs_solar_corrections/index.html

@@ -1692,8 +1692,8 @@ <h2 id="step-one-coordinate-transformation">Step One: Coordinate Transformation<
 <div class="jp-Cell-inputWrapper"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput " data-mime-type="text/markdown">
 <p>Apply coordinate transformations for HMI data products where:</p>
-<p><code>x, y, pd, r, d, mu = coord[i][0], coord[i][1], coord[i][2], coord[i][3], coord[i][4], coord[i][5]<code></p>
-<p><code>wij, nij, rij = vel_coords[i][0], vel_coords[i][1], vel_coords[i][2]<code></p>
+<p><code>x, y, pd, r, d, mu = coord[i][0], coord[i][1], coord[i][2], coord[i][3], coord[i][4], coord[i][5]</code></p>
+<p><code>wij, nij, rij = vel_coords[i][0], vel_coords[i][1], vel_coords[i][2]</code></p>
 
 </div>
 </div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs  ">
@@ -1737,7 +1737,7 @@ <h2 id="step-one-coordinate-transformation">Step One: Coordinate Transformation<
 <div class="jp-Cell-inputWrapper"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput " data-mime-type="text/markdown">
 <p>Remove bad mu values from each map.</p>
-<p><code>hmi_vel, hmi_mag, imap = maps[i][0], maps[i][1], maps[i][2]<code></p>
+<p><code>hmi_vel, hmi_mag, imap = maps[i][0], maps[i][1], maps[i][2]</code></p>
 
 </div>
 </div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs  ">
@@ -1790,7 +1790,7 @@ <h2 id="step-two-calculate-spacecraft-velocity">Step Two: Calculate Spacecraft V
 <div class="jp-Cell-inputWrapper"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput " data-mime-type="text/markdown">
 <p>Calculate relative positions.</p>
-<p><code>deltaw, deltan, deltar, dij = delta[i][0], delta[i][1], delta[i][2], delta[i][3]<code></p>
+<p><code>deltaw, deltan, deltar, dij = delta[i][0], delta[i][1], delta[i][2], delta[i][3]</code></p>
 
 </div>
 </div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs  ">
@@ -2279,7 +2279,7 @@ <h2 id="step-five-unsigned-magnetic-field-strength">Step Five: Unsigned Magnetic
 <p>We calculate radial unsigned magnetic field strength and set pixels with an
 observed magnetic field below the noise value equal to zero.</p>
 <p>The noise level used is from Yeo et al. 2013, and is 8 Gauss.</p>
-<p><code>Bobs, Br = corrected_mag[0], corrected_mag[1]<code></p>
+<p><code>Bobs, Br = corrected_mag[0], corrected_mag[1]</code></p>
 
 </div>
 </div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs  ">
@@ -2524,7 +2524,7 @@ <h3 id="part-one-magnetic-thresholding">Part One: Magnetic Thresholding<a class=
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput " data-mime-type="text/markdown">
 <p>For weighting, we return an active weights array (active = 1) and quiet weights array (active = 0).</p>
 <p>Get threshold maps where:</p>
-<p><code>active, quiet = mag_thresh[i][0], mag_thresh[i][1]<code></p>
+<p><code>active, quiet = mag_thresh[i][0], mag_thresh[i][1]</code></p>
 
 </div>
 </div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs  ">
@@ -2648,7 +2648,7 @@ <h3 id="part-two-intensity-thresholding">Part Two: Intensity Thresholding<a clas
 <div class="jp-Cell-inputWrapper"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput " data-mime-type="text/markdown">
 <p>Calculate intensity threshold value and differentiate between sunspots and faculae where:</p>
-<p><code>fac_inds, spot_inds = int_thresh[0], int_thresh[1]<code></p>
+<p><code>fac_inds, spot_inds = int_thresh[0], int_thresh[1]</code></p>
 
 </div>
 </div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs  ">
@@ -3047,7 +3047,7 @@ <h2 id="step-two-photometric-velocity-due-to-rotational-doppler-imbalance">Step
 <div class="jp-Cell-inputWrapper"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput " data-mime-type="text/markdown">
 <p>Calculate photometric velocity.</p>
-<p><code>v_phot, vphot_bright, vphot_spot = vphot[0], vphot[1], vphot[2]<code></p>
+<p><code>v_phot, vphot_bright, vphot_spot = vphot[0], vphot[1], vphot[2]</code></p>
 
 </div>
 </div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs  ">
@@ -3183,7 +3183,7 @@ <h1 id="magnetic-observables">Magnetic Observables<a class="anchor-link" href="#
 <h2 id="filling-factor">Filling Factor<a class="anchor-link" href="#Filling-Factor">&#182;</a></h2><p>Estimate the disc-averaged filling factors of sunspots and plage:
 $ f_{spot, plage} = \frac{1}{N_{pix}} \sum_{ij} W_{ij} $</p>
 <p>In this case, a weight of 1 is an active pixel (active_weights).</p>
-<p><code>f_bright, f_spot, f = filling[0], filling[1], filling[2]<code></p>
+<p><code>f_bright, f_spot, f = filling[0], filling[1], filling[2]</code></p>
 
 </div>
 </div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs  ">
@@ -3306,7 +3306,7 @@ <h2 id="area-based-observable-calculations">Area Based Observable Calculations<a
 <div class="jp-Cell-inputWrapper"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput " data-mime-type="text/markdown">
 <p>Calculate the area filling factor.</p>
-<p><code>f_small, f_large, f_network, f_plage, f_nonconv = f_area[0], f_area[1], f_area[2], f_area[3], f_area[4]<code></p>
+<p><code>f_small, f_large, f_network, f_plage, f_nonconv = f_area[0], f_area[1], f_area[2], f_area[3], f_area[4]</code></p>
 
 </div>
 </div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs  ">
@@ -3342,7 +3342,7 @@ <h2 id="area-based-observable-calculations">Area Based Observable Calculations<a
 <div class="jp-Cell-inputWrapper"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput " data-mime-type="text/markdown">
 <p>Calculate unsigned flux of various polarized and active regions.</p>
-<p><code>quiet_flux, ar_flux, conv_flux, pol_flux, pol_conv_flux = flux[0], flux[1], flux[2], flux[3], flux[4], flux[5]<code></p>
+<p><code>quiet_flux, ar_flux, conv_flux, pol_flux, pol_conv_flux = flux[0], flux[1], flux[2], flux[3], flux[4], flux[5]</code></p>
 
 </div>
 </div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs  ">
@@ -3380,7 +3380,7 @@ <h2 id="area-based-observable-calculations">Area Based Observable Calculations<a
 <div class="jp-Cell-inputWrapper"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput " data-mime-type="text/markdown">
 <p>Get area weighted convective velocities.</p>
-<p><code>vconv_quiet, vconv_large, vconv_small = vconv_area[0], vconv_area[1], vconv_area[2]<code></p>
+<p><code>vconv_quiet, vconv_large, vconv_small = vconv_area[0], vconv_area[1], vconv_area[2]</code></p>
 
 </div>
 </div><div class="jp-Cell jp-CodeCell jp-Notebook-cell jp-mod-noOutputs  ">

mkdocs/site/examples/docs_sunpy_example/index.html

@@ -1698,9 +1698,9 @@ <h2 id="querying-data">Querying data<a class="anchor-link" href="#Querying-data"
 
 
 
-<div id="4132b656-924c-40ab-859e-79e8cac1261a" class="jupyter-widgets jp-OutputArea-output ">
+<div id="5855610c-7341-4652-aba4-92757f219a37" class="jupyter-widgets jp-OutputArea-output ">
 <script type="text/javascript">
-var element = document.getElementById('4132b656-924c-40ab-859e-79e8cac1261a');
+var element = document.getElementById('5855610c-7341-4652-aba4-92757f219a37');
 </script>
 <script type="application/vnd.jupyter.widget-view+json">
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mkdocs/site/package/calculation_funcs/index.html

@@ -2383,7 +2383,7 @@ <h4 id="sdo_hmi_rvs.tools.calculation_funcs.mag_thresh--returns">Returns</h4>
 
 
 <h2 id="sdo_hmi_rvs.tools.calculation_funcs.map_sequence" class="doc doc-heading">
-<code class="highlight language-python"><span class="n">map_sequence</span><span class="p">(</span><span class="n">dates_list</span><span class="p">,</span> <span class="n">time_range</span><span class="o">=</span><span class="n">datetime</span><span class="o">.</span><span class="n">timedelta</span><span class="p">(</span><span class="n">seconds</span><span class="o">=</span><span class="mi">6</span><span class="p">),</span> <span class="n">instrument</span><span class="o">=&lt;</span><span class="n">sunpy</span><span class="o">.</span><span class="n">net</span><span class="o">.</span><span class="n">attrs</span><span class="o">.</span><span class="n">Instrument</span><span class="p">(</span><span class="n">AIA</span><span class="p">:</span> <span class="n">Atmospheric</span> <span class="n">Imaging</span> <span class="n">Assembly</span><span class="p">)</span> <span class="nb">object</span> <span class="n">at</span> <span class="mh">0x7fcbd5a482b0</span><span class="o">&gt;</span><span class="p">,</span> <span class="n">wavelength</span><span class="o">=&lt;</span><span class="n">sunpy</span><span class="o">.</span><span class="n">net</span><span class="o">.</span><span class="n">attrs</span><span class="o">.</span><span class="n">Wavelength</span><span class="p">(</span><span class="mf">171.0</span><span class="p">,</span> <span class="mf">171.0</span><span class="p">,</span> <span class="s1">&#39;Angstrom&#39;</span><span class="p">)</span><span class="o">&gt;</span><span class="p">)</span></code>
+<code class="highlight language-python"><span class="n">map_sequence</span><span class="p">(</span><span class="n">dates_list</span><span class="p">,</span> <span class="n">time_range</span><span class="o">=</span><span class="n">datetime</span><span class="o">.</span><span class="n">timedelta</span><span class="p">(</span><span class="n">seconds</span><span class="o">=</span><span class="mi">6</span><span class="p">),</span> <span class="n">instrument</span><span class="o">=&lt;</span><span class="n">sunpy</span><span class="o">.</span><span class="n">net</span><span class="o">.</span><span class="n">attrs</span><span class="o">.</span><span class="n">Instrument</span><span class="p">(</span><span class="n">AIA</span><span class="p">:</span> <span class="n">Atmospheric</span> <span class="n">Imaging</span> <span class="n">Assembly</span><span class="p">)</span> <span class="nb">object</span> <span class="n">at</span> <span class="mh">0x7f8677384f70</span><span class="o">&gt;</span><span class="p">,</span> <span class="n">wavelength</span><span class="o">=&lt;</span><span class="n">sunpy</span><span class="o">.</span><span class="n">net</span><span class="o">.</span><span class="n">attrs</span><span class="o">.</span><span class="n">Wavelength</span><span class="p">(</span><span class="mf">171.0</span><span class="p">,</span> <span class="mf">171.0</span><span class="p">,</span> <span class="s1">&#39;Angstrom&#39;</span><span class="p">)</span><span class="o">&gt;</span><span class="p">)</span></code>
 
 
 </h2>

sdo_hmi_rvs/examples/full_pipeline.ipynb

@@ -696,7 +696,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 24,
    "outputs": [
     {
      "data": {
@@ -710,24 +710,26 @@
    "source": [
     "import matplotlib.pyplot as plt\n",
     "\n",
+    "# set up plotting style\n",
+    "plot_style = os.path.join(PlotDir.MPL, 'figure_series.mplstyle')\n",
+    "plt.rcParams['mathtext.fontset'] = 'custom'\n",
+    "plt.rcParams['mathtext.cal'] = 'Helvetica Neue LT Pro'\n",
+    "plt.style.use(plot_style)\n",
+    "\n",
+    "# date to plot\n",
     "date_jd = component_df.date_jd.values\n",
     "x = date_jd - date_jd[0]\n",
-    "\n",
     "y_list = [component_df.f.values, component_df.Bobs.values, component_df.v_conv.values, component_df.v_phot.values,\n",
     "          component_df.rv_model.values - np.median(component_df.rv_model.values)]\n",
+    "\n",
+    "# plot labels\n",
     "xlabel = 'Days since ' + str(int(date_jd[0])) + ' JD'\n",
     "ylabel_list = [r'$\\rm f$' '\\n' r'$\\rm$[%]',\n",
     "               r'$\\rm B_{\\rm obs}$' '\\n' r'$\\rm [G]$',\n",
     "               r'$\\rm v_{\\rm conv}$' '\\n' r'$\\rm[m s^{-1}]$',\n",
     "               r'$\\rm v_{\\rm phot}$' '\\n' r'$\\rm[m s^{-1}]$',\n",
     "               r'$\\rm RV_{\\rm model}$' '\\n' r'$\\rm[m s^{-1}]$']\n",
     "\n",
-    "\n",
-    "plot_style = os.path.join(PlotDir.MPL, 'figure_series.mplstyle')\n",
-    "plt.rcParams['mathtext.fontset'] = 'custom'\n",
-    "plt.rcParams['mathtext.cal'] = 'Helvetica Neue LT Pro'\n",
-    "plt.style.use(plot_style)\n",
-    "\n",
     "# set up figure\n",
     "fig, axs = plt.subplots(len(y_list), 1, sharex='all', figsize=[6, 1.5 * len(y_list)],  gridspec_kw={'hspace': 0})\n",
     "\n",
@@ -740,6 +742,7 @@
     "    yticks = np.arange(y_list[i].min(), y_list[i].max()+0.0002, step=step*2)\n",
     "    axs[i].set(ylim=ylim, yticks=yticks)\n",
     "\n",
+    "# create x-axis ticks and labels\n",
     "axs[i].set(xlabel=xlabel)\n",
     "rng = (x.max() - x.min())\n",
     "step = int(rng/6)\n",
@@ -758,7 +761,11 @@
     "\n",
     "\n",
     "# align y axis labels\n",
-    "fig.align_ylabels(axs)"
+    "fig.align_ylabels(axs)\n",
+    "\n",
+    "# save figure\n",
+    "fig_path = os.path.join(ImgDir.IMG_DIR, 'example_rv_comp.png')\n",
+    "fig.savefig(fig_path)\n"
    ],
    "metadata": {
     "collapsed": false,
@@ -771,9 +778,7 @@
    "cell_type": "code",
    "execution_count": null,
    "outputs": [],
-   "source": [
-    "\n"
-   ],
+   "source": [],
    "metadata": {
     "collapsed": false,
     "pycharm": {

sdo_hmi_rvs/examples/rv_calculation.ipynb

@@ -46,7 +46,7 @@
    "outputs": [],
    "source": [
     "# csv file with rv components\n",
-    "csv_file = os.path.join(CsvDir.CALC, 'csv_name.csv')"
+    "csv_file = os.path.join(CsvDir.CALC, 'example_calcs.csv')"
    ],
    "metadata": {
     "collapsed": false,

sdo_hmi_rvs/tools/settings.py

@@ -32,6 +32,13 @@ class ImgDir:
     IMG_DIR = os.path.join(BaseDir.BASE_DIR, 'images')
 
 
+class PlotDir:
+    """
+    Directories that hold plotting style files
+    """
+    MPL = os.path.join(BaseDir.BASE_DIR, 'mplstyle')
+
+
 class Scaling:
     """
     Class that holds scaling coefficients for RV calculations.
@@ -60,9 +67,3 @@ class NEID(Scaling):
     B = 1.423
     RV0 = -646.076
 
-
-class PlotDir:
-    """
-    Directories that hold plotting style files
-    """
-    MPL = os.path.join(BaseDir.BASE_DIR, 'mplstyle')