Merge pull request #315 from anandxkumar/example

Add: SpecDatabase Example in Gallery

examples/plot_SpecDatabase.py

@@ -0,0 +1,60 @@
+"""
+================================================
+Spectrum Database
+================================================
+RADIS has :py:class:`~radis.tools.database.SpecDatabase` feature used to store and retrieve calculated Spectrums. A path can be specified for SpecDatabase all Spectrums are stored as .spec files which can be loaded
+from the SpecDatabase object itself.  A csv file is generated which contains all input and conditional parameters of Spectrum.
+
+RADIS also has :py:meth:`~radis.lbl.loader.DatabankLoader.init_database` feature which initializes the SpecDatabase for the SpectrumFactory and every Spectrum
+generated from it will be stored in the SpecDatabase automatically.
+
+You can use :py:meth:`~radis.tools.database.SpecList.plot_cond` to make a 2D plot using the conditions of the Spectrums in the SpecDatabase and use a z_label to plot a heat map based on it.
+
+
+"""
+
+from radis import SpectrumFactory
+from radis.tools import SpecDatabase
+
+sf = SpectrumFactory(
+    wavenum_min=2900,
+    wavenum_max=3200,
+    molecule="OH",
+    broadening_max_width=10,  # cm-1
+    medium="vacuum",
+    verbose=0,  # more for more details
+    pressure=10,
+    wstep="auto",
+)
+sf.fetch_databank("hitemp")
+
+# Generating 2 Spectrums
+s1 = sf.eq_spectrum(Tgas=300, path_length=1)
+s2 = sf.eq_spectrum(Tgas=600, path_length=1)
+
+# Creating SpecDatabase
+my_folder = r"/home/pipebomb/Desktop/SpecDatabase_Test/"
+db = SpecDatabase(my_folder, lazy_loading=False)
+
+# Method 1: Creating .spec file
+db.add(s1)
+db.add(s2)
+
+# Method 2: Using init_database()
+sf.init_database(my_folder)
+
+# Generates Spectrum and adds to SpecDatabase automatically
+# Increasing Temperature and decreasing wstep
+wstep_value = 2
+for i in range(900, 3100, 300):
+    wstep_value = wstep_value / 2
+    sf.wstep = wstep_value
+    sf.params.wstep = wstep_value
+    sf.eq_spectrum(Tgas=i, path_length=1)
+
+
+# Loading SpecDatabase
+db_new = SpecDatabase(my_folder)
+
+# Comparing data conditions of different spectrum from csv generated file
+db_new.plot_cond("Tgas", "wstep", "calculation_time")

radis/lbl/loader.py

@@ -1332,6 +1332,7 @@ def init_database(
         """Init a :class:`~radis.tools.database.SpecDatabase` folder in
         ``path`` to later store our spectra. Spectra can also be automatically
         retrieved from the database instead of being calculated.
+
         Parameters
         ----------
         path: str
@@ -1362,6 +1363,9 @@ def init_database(
         -------
         db: SpecDatabase
             the database where spectra will be stored or retrieved
+
+
+        .. minigallery:: radis.lbl.loader.DatabankLoader.init_database
         """
 
         db = SpecDatabase(path, add_info=add_info, add_date=add_date, binary=compress)

radis/tools/database.py

@@ -1668,6 +1668,8 @@ def plot_cond(self, cond_x, cond_y, z_value=None, nfig=None):
 
             >>> db.plot(Tvib, Trot, residual)     # where residual is calculated by a fitting
                                                   # procedure...
+        -------
+        .. minigallery:: radis.tools.database.SpecList.plot_cond
         """
         # %%
 
@@ -1686,17 +1688,21 @@ def plot_cond(self, cond_x, cond_y, z_value=None, nfig=None):
 
         # Overlay color
         if z_value is not None:
-            assert (len(z_value)) == len(self.df)
+            if type(z_value) is str:
+                z = self.df[z_value]
+            else:
+                z = z_value
 
-            z = np.array(z_value) ** 0.5  # because the lower the better
+            assert len(z) == len(self.df)
 
+            z = np.array(z) ** 0.5  # because the lower the better
             #            norm = cm.colors.Normalize(vmax=z.max(), vmin=z.min())
             #            cmap = cm.PRGn
 
             xarr = np.linspace(min(x), max(x))
             yarr = np.linspace(min(y), max(y))
             mx, my = np.meshgrid(xarr, yarr)
-            zgrid = griddata((x, y), z, (mx, my), method="linear")
+            zgrid = griddata((x, y), z, (mx, my), method="nearest")
             levels = np.linspace(min(z), max(z), 20)
             ax.contourf(
                 mx,
@@ -1805,7 +1811,6 @@ class SpecDatabase(SpecList):
         requires all conditions to be either float, string, or boolean. List
         won't work!
 
-
     See Also
     --------
     :func:`~radis.tools.database.load_spec`,
@@ -1827,7 +1832,10 @@ class SpecDatabase(SpecList):
 
     Compare another Spectrum to all spectra in the database:
 
-    :meth:`~radis.tools.database.SpecDatabase.fit_spectrum`,
+    :meth:`~radis.tools.database.SpecDatabase.fit_spectrum`
+
+
+    .. minigallery:: radis.SpecDatabase
     """
 
     def __init__(