Merge pull request #17 from AgPipeline/develop

Merging develop to master - no review
AgPipeline · Oct 15, 2020 · f40710e · f40710e
2 parents fb944b9 + 384cf1e
commit f40710e
Show file tree

Hide file tree

Showing 3 changed files with 37 additions and 22 deletions.
diff --git a/.github/workflows/docker_test_check.sh b/.github/workflows/docker_test_check.sh
@@ -36,8 +36,8 @@ BEGIN {
     FPAT = "([^,]+)|(\"[^\"]+\")"
 }
 {
-  if ($1 != "germplasmName") { # Skipping the header line
-    printf("(%s %s %s %s %s %s %s %s %s %s %s)\n", $9, $10, $11, $12, $13, $14, $15, $16, $17, $18, $19)
+  if ($1 != "species") { # Skipping the header line
+    printf("(%s %s %s %s %s %s %s %s %s %s %s)\n", $8, $9, $10, $11, $12, $13, $14, $15, $16, $17, $18)
   }
 }
 END {

diff --git a/algorithm_rgb.py b/algorithm_rgb.py
@@ -140,14 +140,22 @@ def percent_green(pxarray: np.ndarray) -> float:
     Returns the percentage of an image that is green, which can be used
     to identify plant cover
     """
-    # redness value
-    red = np.sum(pxarray[:, :, 0])
-
-    # greenness value
-    green = np.sum(pxarray[:, :, 1])
-
-    # blueness value
-    blue = np.sum(pxarray[:, :, 2])
+    if pxarray.shape[2] < 4:
+        # Get redness, greenness, and blueness values
+        red = np.sum(pxarray[:, :, 0])
+        green = np.sum(pxarray[:, :, 1])
+        blue = np.sum(pxarray[:, :, 2])
+    else:
+        # Handle Alpha channel masking
+        # Get redness, greenness, and blueness values
+        alpha_mask = np.where(pxarray[:, :, 3] == 0, 1, 0)  # Convert alpha channel to numpy.ma acceptable format
+        channel_masked = np.ma.array(pxarray[:, :, 0], mask=alpha_mask)
+        red = np.ma.sum(channel_masked)
+        channel_masked = np.ma.array(pxarray[:, :, 1], mask=alpha_mask)
+        green = np.ma.sum(channel_masked)
+        channel_masked = np.ma.array(pxarray[:, :, 2], mask=alpha_mask)
+        blue = np.ma.sum(channel_masked)
+        del channel_masked
 
     return round(green / (red + green + blue), 2)
 
@@ -156,16 +164,24 @@ def get_red_green_blue_averages(pxarray: np.ndarray) -> tuple:
     """
     Returns the average red, green, and blue values in a pxarray object
     """
-    # redness value
-    red = np.average(pxarray[:, :, 0])
-
-    # greenness value
-    green = np.average(pxarray[:, :, 1])
-
-    # blueness value
-    blue = np.average(pxarray[:, :, 2])
-
-    return (red, green, blue)
+    if pxarray.shape[2] < 4:
+        # Get redness, greenness, and blueness values
+        red = np.average(pxarray[:, :, 0])
+        green = np.average(pxarray[:, :, 1])
+        blue = np.average(pxarray[:, :, 2])
+    else:
+        # Handle Alpha channel masking
+        # Get redness, greenness, and blueness values
+        alpha_mask = np.where(pxarray[:, :, 3] == 0, 1, 0)  # Convert alpha channel to numpy.ma acceptable format
+        channel_masked = np.ma.array(pxarray[:, :, 0], mask=alpha_mask)
+        red = np.ma.average(channel_masked)
+        channel_masked = np.ma.array(pxarray[:, :, 1], mask=alpha_mask)
+        green = np.ma.average(channel_masked)
+        channel_masked = np.ma.array(pxarray[:, :, 2], mask=alpha_mask)
+        blue = np.ma.average(channel_masked)
+        del channel_masked
+
+    return red, green, blue
 
 
 def calculate(pxarray: np.ndarray) -> list:
@@ -175,7 +191,6 @@ def calculate(pxarray: np.ndarray) -> list:
     Return:
         Returns a list of the calculated values from the
     """
-
     return_list = [excess_greenness_index(pxarray), green_leaf_index(pxarray), cive(pxarray),
                    normalized_difference_index(pxarray), excess_red(pxarray), exgr(pxarray),
                    combined_indices_1(pxarray), combined_indices_2(pxarray), vegetative_index(pxarray),

diff --git a/test_data/experiment.yaml b/test_data/experiment.yaml
@@ -3,7 +3,7 @@
 pipeline:
     studyName: 'S7_20181011'
     season: 'S7_20181011'
-    germplasmName: Sorghum bicolor
+    species: Sorghum bicolor
     collectingSite: Maricopa
     observationTimeStamp: '2018-10-11T13:01:02-08:00'