Getting-started.md

@@ -115,6 +115,11 @@ python exorem_plot.py ./outputs/exorem/corot-4b.h5
 ```
 The figures should be in the _outputs/figures_ directory. 
 
+Alternatively, if you set `output_hdf5 = False` to have ASCII files, you need to execute:
+```bash
+python exorem_plot.py corot-4b --inputs_extension dat
+```
+
 The temperature profile figure (temperature_profile_corot-4b) should look like this:
 
 ![temperature_profile_corot-4b](uploads/f9de76f358104a4af85f9b3e14df8f9c/temperature_profile_corot-4b.png)
@@ -201,7 +206,7 @@ As before, go to the _bin_ directory and execute `./exorem.exe ../inputs/corot-4
 ## Plotting
 Again, let's take a look at our results. Go back to the _exorem_ directory and execute:
 ```bash
-python exorem_plot.py corot-4b_R500
+python exorem_plot.py ./outputs/exorem/corot-4b_R500.h5
 ```
 
 The temperature profile figure (temperature_profile_corot-4b) should look like this:
@@ -226,7 +231,7 @@ Not happy with the figures you get ? What if for example you wanted to see the c
 3. Then, simply do:
     ```python
     plot_contribution_transmission_spectra(
-        './outputs/exorem/spectra_corot-4b_R500.dat', 
+        './outputs/exorem/corot-4b_R500.h5', 
         wvn2wvl=True, 
         xmin=0.5e-6, 
         xmax=1.5e-6, 
@@ -235,9 +240,12 @@ Not happy with the figures you get ? What if for example you wanted to see the c
     ```
 4. If you want to see the effect of the clouds on the transmission spectrum, you can try:
     ```python
-    plot_transmission_spectrum('./outputs/exorem/spectra_corot-4b_R500.dat', wvn2wvl=True, star_radius=814e6, cloud_coverage=0, color='r', label='no cloud')
-    plot_transmission_spectrum('./outputs/exorem/spectra_corot-4b_R500.dat', wvn2wvl=True, star_radius=814e6, cloud_coverage=0.5, color='g', label='50% cover')
-    plot_transmission_spectrum('./outputs/exorem/spectra_corot-4b_R500.dat', wvn2wvl=True, star_radius=814e6, cloud_coverage=1, color='b', label='full cover')
+    plot_transmission_spectrum('./outputs/exorem/example_R50_beta8.h5', wvn2wvl=True, cloud_coverage=0,
+                               color='r', label='no cloud')
+    plot_transmission_spectrum('./outputs/exorem/example_R50_beta8.h5', wvn2wvl=True, cloud_coverage=0.5,
+                               color='g', label='50% cover')
+    plot_transmission_spectrum('./outputs/exorem/example_R50_beta8.h5', wvn2wvl=True, cloud_coverage=1,
+                               color='b', label='full cover')
     plt.xlim([0.3e-6, 2e-6])
     plt.gca().set_xscale('log')
     plt.legend()