Faster runtime of FitModel, refactoring of ReadModel functions, added…

… interpolate_grid, updated tutorials
tomasstolker · Feb 21, 2020 · 0ed28ac · 0ed28ac
1 parent cf2c7a0
commit 0ed28ac
Show file tree

Hide file tree

Showing 16 changed files with 1,320 additions and 909 deletions.
diff --git a/docs/tutorials.rst b/docs/tutorials.rst
@@ -16,7 +16,7 @@ This page contains a list of tutorials which highlight some of the functionaliti
    tutorials/atmospheric_models.ipynb
    tutorials/data_model.ipynb
    tutorials/photometric_calibration.ipynb
-   tutorials/fitting_photometry.ipynb
+   tutorials/fitting_model_spectra.ipynb
 
 .. important::
    A flux calibrated spectrum of Vega is used for the conversion between flux density and magnitude. The magnitude of Vega is set to 0.03 mag for all filters (see also `Stolker et al. 2020 <https://ui.adsabs.harvard.edu/abs/2019arXiv191213316S>`_).
diff --git a/docs/tutorials/atmospheric_models.ipynb b/docs/tutorials/atmospheric_models.ipynb
@@ -40,19 +40,16 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Initiating species v0.1.4... [DONE]\n",
-      "Creating species_config.ini... [DONE]\n",
+      "Initiating species v0.2.0... [DONE]\n",
       "Database: /Users/tomasstolker/applications/species/docs/tutorials/species_database.hdf5\n",
       "Data folder: /Users/tomasstolker/applications/species/docs/tutorials/data\n",
-      "Working folder: /Users/tomasstolker/applications/species/docs/tutorials\n",
-      "Creating species_database.hdf5... [DONE]\n",
-      "Creating data folder... [DONE]\n"
+      "Working folder: /Users/tomasstolker/applications/species/docs/tutorials\n"
      ]
     },
     {
      "data": {
       "text/plain": [
-       "<species.core.setup.SpeciesInit at 0x12d2e4470>"
+       "<species.core.setup.SpeciesInit at 0x124122080>"
       ]
      },
      "execution_count": 2,
@@ -89,7 +86,6 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Downloading DRIFT-PHOENIX model spectra (151 MB)... [DONE]\n",
       "Unpacking DRIFT-PHOENIX model spectra... [DONE]\n",
       "Adding DRIFT-PHOENIX model spectra... [DONE]                     \n"
      ]
@@ -123,14 +119,34 @@
    "cell_type": "code",
    "execution_count": 6,
    "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'teff': (1000.0, 3000.0), 'logg': (3.0, 5.5), 'feh': (-0.6, 0.3)}"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "read_model.get_bounds()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
    "outputs": [],
    "source": [
     "model_param = {'teff':1510., 'logg':4.1, 'feh':0.1}"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -140,7 +156,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -149,18 +165,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Adding filter: MKO/NSFCam.J... [DONE]\n",
-      "Adding filter: MKO/NSFCam.H... [DONE]\n",
-      "Adding filter: MKO/NSFCam.K... [DONE]\n",
-      "Adding filter: MKO/NSFCam.Lp... [DONE]\n",
-      "Adding filter: MKO/NSFCam.Mp... [DONE]\n",
       "Plotting spectrum: model_spectrum.png... [DONE]\n"
      ]
     }
@@ -177,7 +188,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
@@ -187,7 +198,7 @@
        "<IPython.core.display.Image object>"
       ]
      },
-     "execution_count": 10,
+     "execution_count": 11,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -212,7 +223,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
@@ -225,7 +236,7 @@
        " 'feh': array([-0.6, -0.3, -0. ,  0.3])}"
       ]
      },
-     "execution_count": 11,
+     "execution_count": 12,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -243,7 +254,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -252,7 +263,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -262,7 +273,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -271,7 +282,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [
     {
@@ -294,7 +305,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [
     {
@@ -304,7 +315,7 @@
        "<IPython.core.display.Image object>"
       ]
      },
-     "execution_count": 16,
+     "execution_count": 17,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -322,25 +333,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 18,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Adding filter: Paranal/NACO.Mp... [DONE]\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "read_model = species.ReadModel(model='drift-phoenix',\n",
     "                               filter_name='Paranal/NACO.Mp')"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 19,
    "metadata": {},
    "outputs": [
     {
@@ -358,15 +361,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 20,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Downloading Vega spectrum (270 kB)... [DONE]\n",
-      "Adding Vega spectrum... [DONE]\n",
       "Apparent magnitude [mag] = 12.00\n",
       "Absolute magnitude [mag] = 10.50\n"
      ]