Fix readimage import

And update the test to include cmyk channels

Author: NMiklave

plantcv/plantcv/visualize/pixel_scatter_vis.py

@@ -7,7 +7,7 @@
 from plantcv.plantcv import rgb2gray_hsv
 from plantcv.plantcv import rgb2gray_lab
 from plantcv.plantcv import rgb2gray_cmyk
-from plantcv.plantcv import readimage
+from plantcv.plantcv.readimage import readimage
 from plantcv.plantcv import fatal_error
 from plantcv.plantcv import params
 
@@ -101,7 +101,7 @@ def pixel_scatter_plot(paths_to_imgs, x_channel, y_channel):
     fig, ax = plt.subplots()
     # load and plot the set of images sequentially
     for p in paths_to_imgs:
-        img, _, _ = readimage(filename=p, mode="native")
+        img, _, _ = readimage(filename=p)
         h, _, c = img.shape
 
         # resizing to predetermined width to reduce the number of pixels

tests/plantcv/visualize/test_pixel_scatter_plot.py

@@ -2,16 +2,16 @@
 import cv2
 import os
 import numpy as np
-from plantcv.plantcv.visualize.pixel_scatter_vis import pixel_scatter_plot
+from plantcv.plantcv.visualize import pixel_scatter_plot
 
 
-@pytest.mark.parametrize("ch", ['R', 'G', 'B', 'l', 'a', 'b', 'h', 's', 'v', 'gray'])
+@pytest.mark.parametrize("ch", ['R', 'G', 'B', 'l', 'a', 'b', 'h', 's', 'v', 'c', 'm', 'y', 'k', 'gray'])
 def test_pixel_scatter_plot(ch, tmpdir):
     """Test for PlantCV."""
     # Create a tmp directory
     cache_dir = tmpdir.mkdir("cache")
     rng = np.random.default_rng()
-    img_size = (10,10,3)
+    img_size = (10, 10, 3)
     # create a random image and write it to the temp directory
     img = rng.integers(low=0, high=255, size=img_size, dtype=np.uint8, endpoint=True)
     path_to_img = os.path.join(cache_dir, 'tmp_img.png')
@@ -26,12 +26,11 @@ def test_pixel_scatter_plot_wrong_ch(tmpdir):
     # Create a tmp directory
     cache_dir = tmpdir.mkdir("cache")
     rng = np.random.default_rng()
-    img_size = (10,10,3)
+    img_size = (10, 10, 3)
     # create a random image and write it to the temp directory
     img = rng.integers(low=0, high=255, size=img_size, dtype=np.uint8, endpoint=True)
     path_to_img = os.path.join(cache_dir, 'tmp_img.png')
     cv2.imwrite(path_to_img, img)
     # test the function with channel parameter that is not an option
     with pytest.raises(RuntimeError):
         _, _ = pixel_scatter_plot(paths_to_imgs=[path_to_img], x_channel='wrong_ch', y_channel='index')
-