Plot rgb with nan (#693)

* Update sphinx_rtd_theme from 0.5.1 to 0.5.2

* Update sphinx_gallery from 0.8.2 to 0.9.0

* changes to plot nan values earthpy

* added a test

* small formatting

* Update pytest from 6.2.3 to 6.2.4

* Update tox from 3.23.0 to 3.23.1

* Update sphinx from 3.5.3 to 4.0.2

* Update pre-commit from 2.11.1 to 2.13.0

* Update pytest-cov from 2.11.1 to 2.12.1

* Added very basic Check CRS function.

* Update importlib-metadata from 3.10.0 to 4.5.0 (#706)

Co-authored-by: pyup-bot <github-bot@pyup.io>

earthpy/plot.py

@@ -331,7 +331,7 @@ def _stretch_im(arr, str_clip):
     s_max = 100 - str_clip
     arr_rescaled = np.zeros_like(arr)
     for ii, band in enumerate(arr):
-        lower, upper = np.percentile(band, (s_min, s_max))
+        lower, upper = np.nanpercentile(band, (s_min, s_max))
         arr_rescaled[ii] = exposure.rescale_intensity(
             band, in_range=(lower, upper)
         )
@@ -405,6 +405,11 @@ def plot_rgb(
     if stretch:
         rgb_bands = _stretch_im(rgb_bands, str_clip)
 
+    nan_check = np.isnan(rgb_bands)
+
+    if np.any(nan_check):
+        rgb_bands = np.ma.masked_array(rgb_bands, nan_check)
+
     # If type is masked array - add alpha channel for plotting
     if ma.is_masked(rgb_bands):
         # Build alpha channel
@@ -582,7 +587,11 @@ def hist(
             hist_range = (np.nanmin(arr_comp), np.nanmax(arr_comp))
         fig, ax = plt.subplots(figsize=figsize)
         ax.hist(
-            arr_comp, range=hist_range, bins=bins, color=colors[0], alpha=alpha
+            arr_comp,
+            range=hist_range,
+            bins=bins,
+            color=colors[0],
+            alpha=alpha,
         )
         if title:
             ax.set(title=title[0])

earthpy/tests/test_plot_rgb.py

@@ -132,6 +132,22 @@ def test_stretch_image(rgb_image):
     plt.close()
 
 
+def test_stretch_image_nan(rgb_image):
+    """Test that running stretch actually stretches the data
+    to a max value of 255 and min value of 0 when nan values
+    are present within the plot_rgb fun."""
+
+    im, _ = rgb_image
+    np.place(im, im > 150, [0])
+    im = np.where(im < 25, np.nan, im)
+
+    ax = plot_rgb(im, stretch=True)
+    max_val = ax.get_images()[0].get_array().max()
+    min_val = ax.get_images()[0].get_array().min()
+    assert max_val == 255 and min_val == 0
+    plt.close()
+
+
 def test_masked_im(rgb_image):
     """Test that a masked image will be plotted using an alpha channel.
     Thus it should return an array that has a 4th dimension representing