Updated tutorials, added backward compatibility for the det_type attr…

…ibute
tomasstolker · Aug 4, 2020 · 660f70a · 660f70a
1 parent b998137
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Showing 7 changed files with 372 additions and 152 deletions.
diff --git a/docs/tutorials/atmospheric_models.ipynb b/docs/tutorials/atmospheric_models.ipynb
diff --git a/docs/tutorials/flux_magnitude.ipynb b/docs/tutorials/flux_magnitude.ipynb
@@ -38,15 +38,18 @@
      "output_type": "stream",
      "text": [
       "Initiating species v0.3.1... [DONE]\n",
+      "Creating species_config.ini... [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"
+      "Working folder: /Users/tomasstolker/applications/species/docs/tutorials\n",
+      "Creating species_database.hdf5... [DONE]\n",
+      "Creating data folder... [DONE]\n"
      ]
     },
     {
      "data": {
       "text/plain": [
-       "<species.core.setup.SpeciesInit at 0x10e35c550>"
+       "<species.core.setup.SpeciesInit at 0x1087e0630>"
       ]
      },
      "execution_count": 1,
@@ -77,7 +80,15 @@
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Adding filter: JWST/NIRCam.F115W... [DONE]\n"
+     ]
+    }
+   ],
    "source": [
     "synphot = species.SyntheticPhotometry('JWST/NIRCam.F115W')"
    ]
@@ -98,6 +109,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
+      "Downloading Vega spectrum (270 kB)... [DONE]\n",
+      "Adding Vega spectrum... [DONE]\n",
       "Flux (W m-2 um-1) = 4.08e-15 +/- 7.56e-16\n"
      ]
     }
@@ -145,7 +158,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "As expected, we obtain again the magnitude that we start out with."
+    "As expected, we obtain again the magnitude that we started out with."
    ]
   },
   {

diff --git a/docs/tutorials/running_species.ipynb b/docs/tutorials/running_species.ipynb
diff --git a/docs/tutorials/spectral_library.ipynb b/docs/tutorials/spectral_library.ipynb
diff --git a/docs/tutorials/synthetic_photometry.ipynb b/docs/tutorials/synthetic_photometry.ipynb
diff --git a/species/plot/plot_color.py b/species/plot/plot_color.py
@@ -69,12 +69,14 @@ def plot_color_magnitude(boxes: list,
         to None.
     companion_labels : bool
         Plot labels with the names of the directly imaged companions.
-    reddening : list(tuple(str, str, str, float, str, float, tuple(float, float)), None
+    reddening : list(tuple(tuple(str, str), tuple(str, float), str, float, tuple(float, float)), None
         Include reddening arrows by providing a list with tuples. Each tuple contains the filter
-        names for the color, the filter name for the magnitude, the particle radius (um), and the
-        start position (color, mag) of the arrow in the plot, so (filter_color_1, filter_color_2,
-        filter_mag, composition, radius, (x_pos, y_pos)). The composition can be either 'Fe' or
-        'MgSiO3' (both with crystalline structure). The parameter is not used if set to ``None``.
+        names for the color, the filter name and value of the magnitude, the particle radius (um),
+        and the start position (color, mag) of the arrow in the plot, so ``((filter_color_1,
+        filter_color_2), (filter_mag, mag_value), composition, radius, (x_pos, y_pos))``. The
+        composition can be either ``'Fe'`` or ``'MgSiO3'`` (both with crystalline structure). Both
+        ``xlim`` and ``ylim`` need to be set for the correct rotation of the reddening label. The
+        parameter is not used if set to ``None``.
     field_range : tuple(str, str), None
         Range of the discrete colorbar for the field dwarfs. The tuple should contain the lower
         and upper value ('early M', 'late M', 'early L', 'late L', 'early T', 'late T', 'early Y).

diff --git a/species/read/read_filter.py b/species/read/read_filter.py
@@ -3,6 +3,7 @@
 """
 
 import os
+import warnings
 import configparser
 
 from typing import Union, Tuple
@@ -167,6 +168,15 @@ def detector_type(self) -> str:
 
         with h5py.File(self.database, 'r') as h5_file:
             dset = h5_file[f'filters/{self.filter_name}']
-            det_type = dset.attrs['det_type']
+
+            if 'det_type' in dset.attrs:
+                det_type = dset.attrs['det_type']
+
+            else:
+                warnings.warn('Detector type not found. The database was probably created '
+                              'before the detector type was introduced in species (v0.3.1). '
+                              'Assuming an energy-counting detector.')
+
+                det_type = 'energy'
 
         return det_type