restructured example dir and seperated peak analysis into three distinct files

Author: Angelus Vincent

examples/data_cleaning/README.rst

@@ -1,4 +1,4 @@
-Data Processing
+Data Processing 
 ===============
 
-Gallery of examples for data processing in lumispy/hyperspy.
+Below is a gallery of examples on how to proccess data.

examples/data_cleaning/data_smoothing.py

@@ -5,40 +5,46 @@
 This example shows how to smooth a dataset.
 """
 
+# %%
+# Load the data
 import lumispy as lum
 
-# Load the data
 cl1 = lum.data.asymmetric_peak_map()
 cl1 = cl1.remove_background(signal_range=(550.0, 620.0), background_type="Offset")
 cl1 = cl1.isig[:-3]
 cl1.spikes_removal_tool(interactive=False)
 
-cl3 = cl1.deepcopy()
+cl3 = lum.data.asymmetric_peak_map()
 cl3 = cl3.remove_background(signal_range=(550.0, 620.0), background_type="Offset")
 cl3 = cl3.isig[:-3]
 cl3.spikes_removal_tool(interactive=False)
 
-
+# %%
 # Display the original data
 
 cl1.inav[0, 0].plot()
 
+# %%
 # The current dataset is quite noisy. As the peak is broad in comparison with the spectral resolution.
 # One way to improve that is by rebinning the data along the signal axis:
 
 cl2 = cl1.rebin(scale=[1, 1, 2])
 
+# %%
 # Display the smoothed data
 
 cl2.inav[0, 0].plot()
 
+# %%
 # Another way to smooth
 
 cl3.smooth_lowess(smoothing_parameter=0.1, number_of_iterations=2)
 
+# %%
 # Display the data
 
 cl3.inav[0, 0].plot()
 
-# %%
+# sphinx_gallery_start_ignore
 # sphinx_gallery_thumbnail_number = 3
+# sphinx_gallery_end_ignore

examples/data_cleaning/remove_background.py

@@ -5,25 +5,27 @@
 This example removes the background from a dataset.
 """
 
+# %%
+# Load the data
 import lumispy as lum
 import matplotlib.pyplot as plt
 
-# Load the data
 cl1 = lum.data.asymmetric_peak_map()
 
+# %%
 # Display the original data
 
 cl1.plot()
 plt.close(1)
 
-# Now we remove the background
+# %%
+# Now we remove the background and display the data
 
 cl2 = cl1.remove_background(signal_range=(550.0, 620.0), background_type="Offset")
 
-# Display the background removed data
-
 cl2.plot()
-plt.close(3)
+plt.close(1)
 
-# %%
+# sphinx_gallery_start_ignore
 # sphinx_gallery_thumbnail_number = 2
+# sphinx_gallery_end_ignore

examples/data_cleaning/remove_pixels.py

@@ -5,25 +5,31 @@
 This example removes pixels from a dataset.
 """
 
+# %%
+# Load the data
 import lumispy as lum
 import matplotlib.pyplot as plt
 
-# Load the data
 cl1 = lum.data.asymmetric_peak_map()
 cl1 = cl1.remove_background(signal_range=(550.0, 620.0), background_type="Offset")
 
+# %%
 # Display the original data
 
 cl1.plot()
 plt.close(1)
 
+# %%
 # The signal beyond 800 nm goes to negative values, so lets remove the last three pixels from every spectrum:
 
 cl2 = cl1.isig[:-3]
 
+# %%
 # Display cleaned data
 
 cl2.plot()
-plt.close(3)
-# %%
+plt.close(1)
+
+# sphinx_gallery_start_ignore
 # sphinx_gallery_thumbnail_number = 2
+# sphinx_gallery_end_ignore

examples/data_cleaning/remove_spikes.py

@@ -5,23 +5,29 @@
 This example shows how to remove spikes from a dataset.
 """
 
+# %%
+# Load the data
 import lumispy as lum
 
-# Load the data
 cl1 = lum.data.asymmetric_peak_map()
 cl1 = cl1.remove_background(signal_range=(550.0, 620.0), background_type="Offset")
 cl1 = cl1.isig[:-3]
 
+# %%
 # Display the original data
 
 cl1.inav[29, 0].plot()
 
+# %%
 # As seen there is a heavy spike, so lets remove it:
 
 cl1.spikes_removal_tool(interactive=False)
 
+# %%
 # Display cleaned data
 
 cl1.inav[29, 0].plot()
-# %%
+
+# sphinx_gallery_start_ignore
 # sphinx_gallery_thumbnail_number = 2
+# sphinx_gallery_end_ignore