better solution

Author: JeremyPike

episodes/07-thresholding.md

@@ -616,9 +616,8 @@ and label from the image before applying Otsu's method.
 ## Solution
 
 We can apply a simple binary thresholding with a threshold
-`t=0.95` to remove the label and circle from the image. We use the
-binary mask to set the pixels in the blurred image to zero
-(black).
+`t=0.95` to remove the label and circle from the image. We can then use the
+binary mask to calculate the Otsu threshold without the pixels from the label and circle.
 
 ```python
 def enhanced_root_mass(filename, sigma):
@@ -631,21 +630,22 @@ def enhanced_root_mass(filename, sigma):
 
     # perform binary thresholding to mask the white label and circle
     binary_mask = blurred_image < 0.95
-    # use the mask to remove the circle and label from the blurred image
-    blurred_image[~binary_mask] = 0
-
-    # perform automatic thresholding to produce a binary image
-    t = ski.filters.threshold_otsu(blurred_image)
-    binary_mask = blurred_image > t
+    
+    # perform automatic thresholding using only the pixels with value True in the binary mask
+    t = ski.filters.threshold_otsu(blurred_image[binary_mask])
+    
+    # update binary mask to identify pixels which are both less than 0.95 and greater than t
+    binary_mask = np.logical_and(binary_mask, blurred_image > t)
 
     # determine root mass ratio
-    rootPixels = np.count_nonzero(binary_mask)
+    root_pixels = np.count_nonzero(binary_mask)
     w = binary_mask.shape[1]
     h = binary_mask.shape[0]
-    density = rootPixels / (w * h)
+    density = root_pixels / (w * h)
 
     return density
 
+
 all_files = glob.glob("data/trial-*.jpg")
 for filename in all_files:
     density = enhanced_root_mass(filename=filename, sigma=1.5)
@@ -657,10 +657,10 @@ The output of the improved program does illustrate that the white circles
 and labels were skewing our root mass ratios:
 
 ```output
-data/trial-016.jpg,0.045935837765957444
-data/trial-020.jpg,0.058800033244680854
-data/trial-216.jpg,0.13705003324468085
-data/trial-293.jpg,0.13164461436170213
+data\trial-016.jpg,0.046250166223404256
+data\trial-020.jpg,0.05886968085106383
+data\trial-216.jpg,0.13712117686170214
+data\trial-293.jpg,0.13190342420212767
 ```
 
 Here are the binary images produced by the additional thresholding.