use load_image

jcvi/graphics/base.py

@@ -194,7 +194,10 @@ def linear_shade(from_color, fraction=0.5):
     return linear_blend(from_color, "w", fraction)
 
 
-def load_image(filename):
+def load_image(filename: str) -> np.ndarray:
+    """
+    Load an image file and return as numpy array.
+    """
     img = plt.imread(filename)
     if len(img.shape) == 2:  # Gray-scale image, convert to RGB
         # http://www.socouldanyone.com/2013/03/converting-grayscale-to-rgb-with-numpy.html

jcvi/projects/jcvi.py

@@ -14,7 +14,7 @@
 from ..assembly.hic import draw_hic_heatmap
 from ..assembly.kmer import draw_ks_histogram
 from ..compara.pedigree import Pedigree, calculate_inbreeding
-from ..graphics.base import normalize_axes, panel_labels, plt, savefig
+from ..graphics.base import load_image, normalize_axes, panel_labels, plt, savefig
 from ..graphics.chromosome import draw_chromosomes
 from ..graphics.landscape import draw_multi_depth
 
@@ -54,7 +54,7 @@ def diversity(args):
     logger.info("Pedigree graph written to `%s`", pngfile)
 
     # Show the image as is
-    ax1_root.imshow(plt.imread(pngfile))
+    ax1_root.imshow(load_image(pngfile))
     ax1_root.set_axis_off()
 
     # Panel B