Merge pull request #10 from danforthcenter/get_centroid

Get centroids

docs/get_centroids.md

@@ -0,0 +1,44 @@
+## Get Centroids 
+
+Extract the centroid coordinate (column,row) from regions in a binary image. 
+
+**plantcv.annotate.get_centroids**(*bin_img*)
+
+**returns** list containing coordinates of centroids 
+
+- **Parameters:**
+    - bin_img - Binary image containing the connected regions to consider
+- **Context:**
+    - Given an arbitrary mask of the objects of interest, `get_centroids`
+    returns a list of coordinates that can the be imported into the annotation class [Points](Points.md).
+
+- **Example use:**
+    - Below
+
+**Binary image**
+
+![count_img](img/documentation_images/get_centroids/discs_mask.png)
+
+```python
+
+from plantcv import plantcv as pcv
+
+# Set global debug behavior to None (default), "print" (to file),
+# or "plot"
+pcv.params.debug = "plot"
+
+# Apply get centroids to the binary image
+coords = pcv.annotate.get_centroids(bin_img=binary_img)
+print(coords)
+# [[1902, 600], [1839, 1363], [1837, 383], [1669, 1977], [1631, 1889], [1590, 1372], [1550, 1525],
+# [1538, 1633], [1522, 1131], [1494, 2396], [1482, 1917], [1446, 1808], [1425, 726], [1418, 2392],
+# [1389, 198], [1358, 1712], [1288, 522], [1289, 406], [1279, 368], [1262, 1376], [1244, 1795],
+# [1224, 1327], [1201, 624], [1181, 725], [1062, 85], [999, 840], [885, 399], [740, 324], [728, 224],
+# [697, 860], [660, 650], [638, 2390], [622, 1565], [577, 497], [572, 2179], [550, 2230], [547, 1826],
+# [537, 892], [538, 481], [524, 2144], [521, 2336], [497, 201], [385, 1141], [342, 683], [342, 102],
+# [332, 1700], [295, 646], [271, 60], [269, 1626], [210, 1694], [189, 878], [178, 1570], [171, 2307],
+# [61, 286], [28, 2342]]
+
+```
+
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv-annotate/blob/main/plantcv/annotate/get_centroids.py)

mkdocs.yml

@@ -18,6 +18,7 @@ nav:
   - 'PlantCV Namespace':
     - 'Annotation Tools':
       - Points: Points.md
+      - Get Centroids: get_centroids.md
 markdown_extensions:
   - toc:
       permalink: True

plantcv/annotate/__init__.py

@@ -1,9 +1,11 @@
 from importlib.metadata import version
 from plantcv.annotate.classes import Points
+from plantcv.annotate.get_centroids import get_centroids
 
 # Auto versioning
 __version__ = version("plantcv-annotate")
 
 __all__ = [
-    "Points"
+    "Points",
+    "get_centroids"
     ]

plantcv/annotate/get_centroids.py

@@ -0,0 +1,28 @@
+# Get centroids from mask objects
+
+from skimage.measure import label, regionprops
+
+
+def get_centroids(bin_img):
+    """Get the coordinates (row,column) of the centroid of each connected region in a binary image.
+
+    Inputs:
+    bin_img         = Binary image containing the connected regions to consider
+
+    Returns:
+    coords          = List of coordinates (row,column) of the centroids of the regions
+
+    :param bin_img: numpy.ndarray
+    :return coords: list
+    """
+    # find contours in the binary image
+    labeled_img = label(bin_img)
+    # measure regions
+    obj_measures = regionprops(labeled_img)
+    coords = []
+    for obj in obj_measures:
+        # Convert coord values to int
+        coord = tuple(map(int, obj.centroid))
+        coords.append(coord)
+
+    return coords

tests/conftest.py

@@ -15,6 +15,8 @@ def __init__(self):
         self.snapshot_dir = os.path.join(self.datadir, "snapshot_dir")
         # RGB image
         self.small_rgb_img = os.path.join(self.datadir, "setaria_small_plant_rgb.png")
+        # Binary image
+        self.small_bin_img = os.path.join(self.datadir, "setaria_small_plant_mask.png")
         # Text file with tuple coordinates (by group label)
         self.pollen_coords = os.path.join(self.datadir, "points_file_import.coords")
 

tests/test_annotate_get_centroids.py

@@ -0,0 +1,12 @@
+import cv2
+from plantcv.annotate.get_centroids import get_centroids
+
+
+def test_get_centroids(test_data):
+    """Test for PlantCV."""
+    # Read in test data
+    mask = cv2.imread(test_data.small_bin_img, -1)
+
+    coor = get_centroids(bin_img=mask)
+
+    assert coor == [(166, 214)]