Update to use script to generate doc images

README.rst

@@ -220,7 +220,7 @@ any identified peaks, reflecting periodic components.
 
 Example output for the report of a FOOOF fit on an individual power spectrum:
 
-.. image:: https://raw.githubusercontent.com/fooof-tools/fooof/master/doc/img/FOOOF_report.png
+.. image:: https://raw.githubusercontent.com/fooof-tools/fooof/master/doc/img/FOOOF_report.pdf
 
 **Defining the model Settings**
 
@@ -264,7 +264,7 @@ We can fit this  which can be fit as:
 
 Example output from using FOOOFGroup across a group of power spectra:
 
-.. image:: https://raw.githubusercontent.com/fooof-tools/fooof/master/doc/img/FOOOFGroup_report.png
+.. image:: https://raw.githubusercontent.com/fooof-tools/fooof/master/doc/img/FOOOFGroup_report.pdf
 
 **Other Functionality**
 

doc/Makefile

@@ -31,7 +31,10 @@ check:
 	make SPHINXOPTS="-n" html
 	make linkcheck
 
-## make install:
+# Create the plots used in the FOOOF documentation
+plots:
+	python make_doc_plots.py
+
 # Build the html site, and push it to gh-pages branch of repo to deploy
 install:
 	rm -rf _build/doctrees _build/tmp_html

doc/conf.py

@@ -132,7 +132,7 @@
                                         '../motivations/concepts',
                                         '../motivations/measurements']),
     'within_subsection_order': FileNameSortKey,
-    'default_thumb_file': 'img/spectrum.png',
+    'default_thumb_file': 'img/spectrum.pdf',
     'backreferences_dir': 'generated',   # Where to drop linking files between examples & API
     'doc_module': ('fooof',),
     'reference_url': {'fooof': None}

doc/make_doc_plots.py

@@ -0,0 +1,75 @@
+"""Create the images for the FOOOF documentation."""
+
+import shutil
+
+import numpy as np
+import matplotlib.pyplot as plt
+
+from fooof import FOOOF, FOOOFGroup
+from fooof.sim.gen import gen_power_spectrum
+from fooof.plts.utils import check_ax
+from fooof.plts.spectra import plot_spectrum
+from fooof.utils.download import load_fooof_data
+
+###################################################################################################
+###################################################################################################
+
+def main():
+
+    ## Individual Model Plot
+
+    # Download examples data files needed for this example
+    freqs = load_fooof_data('freqs.npy', folder='data')
+    spectrum = load_fooof_data('spectrum.npy', folder='data')
+
+    # Initialize and fit an example power spectrum model
+    fm = FOOOF(peak_width_limits=[1, 6], max_n_peaks=6, min_peak_height=0.2, verbose=False)
+    fm.fit(freqs, spectrum, [3, 40])
+
+    # Save out the report
+    fm.save_report('FOOOF_report.pdf', 'img')
+
+    ## Group Plot
+
+    # Download examples data files needed for this example
+    freqs = load_fooof_data('group_freqs.npy', folder='data')
+    spectra = load_fooof_data('group_powers.npy', folder='data')
+
+    # Initialize and fit a group of example power spectrum models
+    fg = FOOOFGroup(peak_width_limits=[1, 6], max_n_peaks=6, min_peak_height=0.2, verbose=False)
+    fg.fit(freqs, spectra, [3, 30])
+
+    # Save out the report
+    fg.save_report('FOOOFGroup_report.pdf', 'img')
+
+    ## Make the icon plot
+
+    # Simulate an example power spectrum
+    fs, ps = gen_power_spectrum([4, 35], [0, 1], [[10, 0.3, 1],[22, 0.15, 1.25]], nlv=0.01)
+
+    def custom_style(ax, log_freqs, log_powers):
+        """Custom styler-function for the icon plot."""
+
+        # Set the top and right side frame & ticks off
+        ax.spines['right'].set_visible(False)
+        ax.spines['top'].set_visible(False)
+
+        # Set linewidth of remaining spines
+        ax.spines['left'].set_linewidth(10)
+        ax.spines['bottom'].set_linewidth(10)
+        ax.set_xticks([], [])
+        ax.set_yticks([], [])
+
+    # Create and save out the plot
+    plot_spectrum(fs, ps, log_freqs=False, log_powers=True, lw=12, alpha=0.8,
+                  color='grey', plot_style=custom_style, ax=check_ax(None, [6, 6]))
+    plt.tight_layout()
+    plt.savefig('img/spectrum.pdf')
+
+    ## Clean Up
+
+    # Remove the data folder
+    shutil.rmtree('data')
+
+if __name__ == "__main__":
+    main()