From ac60d30ef69bdb0099219cbf63dc3a1610f03b28 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Tue, 17 Dec 2024 14:34:25 -0600
Subject: [PATCH 01/36] Create segment_ends.py

---
 plantcv/plantcv/morphology/segment_ends.py | 65 ++++++++++++++++++++++
 1 file changed, 65 insertions(+)
 create mode 100644 plantcv/plantcv/morphology/segment_ends.py

diff --git a/plantcv/plantcv/morphology/segment_ends.py b/plantcv/plantcv/morphology/segment_ends.py
new file mode 100644
index 000000000..86f4a8b30
--- /dev/null
+++ b/plantcv/plantcv/morphology/segment_ends.py
@@ -0,0 +1,65 @@
+# Find both segment end coordinates 
+import os
+import cv2
+import numpy as np
+from plantcv.plantcv import params
+from plantcv.plantcv._debug import _debug
+from plantcv.plantcv.morphology import _iterative_prune
+from plantcv.plantcv._helpers import _cv2_findcontours
+
+
+def segment_ends(objects, mask=None, label=None):
+    """Find tips in skeletonized image.
+    The endpoints algorithm was inspired by Jean-Patrick Pommier: https://gist.github.com/jeanpat/5712699
+
+    Inputs:
+    skel_img    = Skeletonized image
+    mask        = (Optional) binary mask for debugging. If provided, debug image will be overlaid on the mask.
+    label       = Optional label parameter, modifies the variable name of
+                  observations recorded (default = pcv.params.sample_label).
+    Returns:
+    tip_img   = Image with just tips, rest 0
+
+    :param skel_img: numpy.ndarray
+    :param mask: numpy.ndarray
+    :param label: str
+    :return tip_img: numpy.ndarray
+    """
+    
+    mask_copy = mask.copy()
+    leaf_objects = objects
+    tip_plot = cv2.cvtColor(mask_copy, cv2.COLOR_GRAY2RGB)
+    segment_end_objs1 = [] 
+    segment_end_objs2 = [] 
+
+    # Find segment end coordinates
+    for i, cnt in enumerate(leaf_objects):
+        # Draw leaf objects
+        find_segment_tangents = np.zeros(mask.shape[:2], np.uint8)
+        cv2.drawContours(find_segment_tangents, leaf_objects, i, 255, 1, lineType=8)
+        # Prune back ends of leaves
+        pruned_segment = _iterative_prune(find_segment_tangents, 1)
+        # Segment ends are the portions pruned off
+        segment_ends = find_segment_tangents - pruned_segment
+        segment_end_obj, _ = _cv2_findcontours(bin_img=segment_ends)
+        segment_end_objs1.append(segment_end_obj[0])
+        segment_end_objs2.append(segment_end_obj[1])
+        
+    # Initialize list of tip data points
+    tip_list = []
+    labels = []
+    inner_list = [] 
+    for i, coor in enumerate(segment_end_objs1):
+        x, y = coor.ravel()[:2]
+        coord = (int(x), int(y))
+        inner_list.append(coord)
+        print(coord)
+        labels.append(i)
+        cv2.drawContours(tip_plot, leaf_objects, i, (150, 150, 150), params.line_thickness, lineType=8)  # segments
+        cv2.circle(tip_plot, (x, y), params.line_thickness, (50, 0, 255), -1)  # Red auricles
+        tip = segment_end_objs2[i]
+        x, y = tip.ravel()[:2]
+        coord = (int(x), int(y))
+        tip_list.append(coord)
+        cv2.circle(tip_plot, (x, y), params.line_thickness, (0, 255, 0), -1)  # green tips
+    _debug(visual=tip_plot, filename=os.path.join(params.debug_outdir, f"{params.device}_segment_ends.png"))

From a5ef615e60f70901bb1f9b2eebc5d57dfbced46c Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Tue, 17 Dec 2024 14:39:29 -0600
Subject: [PATCH 02/36] range rather than enumerate

---
 plantcv/plantcv/morphology/segment_ends.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plantcv/plantcv/morphology/segment_ends.py b/plantcv/plantcv/morphology/segment_ends.py
index 86f4a8b30..9d8ea1da6 100644
--- a/plantcv/plantcv/morphology/segment_ends.py
+++ b/plantcv/plantcv/morphology/segment_ends.py
@@ -33,7 +33,7 @@ def segment_ends(objects, mask=None, label=None):
     segment_end_objs2 = [] 
 
     # Find segment end coordinates
-    for i, cnt in enumerate(leaf_objects):
+    for i in range(len(leaf_objects)):
         # Draw leaf objects
         find_segment_tangents = np.zeros(mask.shape[:2], np.uint8)
         cv2.drawContours(find_segment_tangents, leaf_objects, i, 255, 1, lineType=8)

From 269137a43018ec8d05e281d7ffc2cc78886ee997 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Wed, 18 Dec 2024 15:36:32 -0600
Subject: [PATCH 03/36] helper for _find_tips

avoid saving to outputs in the helper function but produce the same relevant outputs, update instances of find_tips getting used throughout morphology
---
 .../plantcv/morphology/_iterative_prune.py    |  4 +-
 plantcv/plantcv/morphology/find_tips.py       | 38 +++++++++++++++----
 .../plantcv/morphology/segment_curvature.py   |  4 +-
 3 files changed, 34 insertions(+), 12 deletions(-)

diff --git a/plantcv/plantcv/morphology/_iterative_prune.py b/plantcv/plantcv/morphology/_iterative_prune.py
index 4816bfdb1..e1f51e128 100644
--- a/plantcv/plantcv/morphology/_iterative_prune.py
+++ b/plantcv/plantcv/morphology/_iterative_prune.py
@@ -2,7 +2,7 @@
 import numpy as np
 from plantcv.plantcv import params
 from plantcv.plantcv import image_subtract
-from plantcv.plantcv.morphology import find_tips
+from plantcv.plantcv.morphology import _find_tips
 from plantcv.plantcv._helpers import _cv2_findcontours
 
 
@@ -26,7 +26,7 @@ def _iterative_prune(skel_img, size):
 
     # Iteratively remove endpoints (tips) from a skeleton
     for _ in range(0, size):
-        endpoints = find_tips(pruned_img)
+        endpoints, _, _ = _find_tips(pruned_img)
         pruned_img = image_subtract(pruned_img, endpoints)
 
     # Make debugging image
diff --git a/plantcv/plantcv/morphology/find_tips.py b/plantcv/plantcv/morphology/find_tips.py
index 4d40c5c19..07791201f 100644
--- a/plantcv/plantcv/morphology/find_tips.py
+++ b/plantcv/plantcv/morphology/find_tips.py
@@ -9,8 +9,8 @@
 from plantcv.plantcv._helpers import _cv2_findcontours
 
 
-def find_tips(skel_img, mask=None, label=None):
-    """Find tips in skeletonized image.
+def _find_tips(skel_img, mask=None):
+    """Helper function to find tips in skeletonized image.
     The endpoints algorithm was inspired by Jean-Patrick Pommier: https://gist.github.com/jeanpat/5712699
 
     Inputs:
@@ -79,12 +79,34 @@ def find_tips(skel_img, mask=None, label=None):
         tip_labels.append(i)
         cv2.circle(tip_plot, (x, y), params.line_thickness, (0, 255, 0), -1)
 
-    outputs.add_observation(sample=label, variable='tips', trait='list of tip coordinates identified from a skeleton',
-                            method='plantcv.plantcv.morphology.find_tips', scale='pixels', datatype=list,
-                            value=tip_list, label=tip_labels)
-
     # Reset debug mode
     params.debug = debug
-    _debug(visual=tip_plot, filename=os.path.join(params.debug_outdir, f"{params.device}_skeleton_tips.png"))
 
-    return tip_img
+    return tip_img, tip_list, tip_labels
+
+def find_tips(skel_img, mask=None, label=None):
+    """Find tips in skeletonized image.
+    The endpoints algorithm was inspired by Jean-Patrick Pommier: https://gist.github.com/jeanpat/5712699
+
+    Inputs:
+    skel_img    = Skeletonized image
+    mask        = (Optional) binary mask for debugging. If provided, debug image will be overlaid on the mask.
+    label       = Optional label parameter, modifies the variable name of
+                  observations recorded (default = pcv.params.sample_label).
+    Returns:
+    tip_img   = Image with just tips, rest 0
+
+    :param skel_img: numpy.ndarray
+    :param mask: numpy.ndarray
+    :param label: str
+    :return tip_img: numpy.ndarray
+    """
+    tip_img, tip_list, tip_labels = _find_tips(skel_img=skel_img, mask=mask)
+
+    _debug(visual=tip_img, filename=os.path.join(params.debug_outdir, f"{params.device}_skeleton_tips.png"))
+    # Save coordinates to Outputs 
+    outputs.add_observation(sample=label, variable='tips', trait='list of tip coordinates identified from a skeleton',
+                            method='plantcv.plantcv.morphology.find_tips', scale='pixels', datatype=list,
+                            value=tip_list, label=tip_labels)
+    
+    return tip_img
\ No newline at end of file
diff --git a/plantcv/plantcv/morphology/segment_curvature.py b/plantcv/plantcv/morphology/segment_curvature.py
index 8e7b3a413..c44cacba6 100644
--- a/plantcv/plantcv/morphology/segment_curvature.py
+++ b/plantcv/plantcv/morphology/segment_curvature.py
@@ -5,7 +5,7 @@
 from plantcv.plantcv import params
 from plantcv.plantcv import outputs
 from plantcv.plantcv import color_palette
-from plantcv.plantcv.morphology import find_tips
+from plantcv.plantcv.morphology import _find_tips
 from plantcv.plantcv.morphology import segment_path_length
 from plantcv.plantcv.morphology import segment_euclidean_length
 from plantcv.plantcv._debug import _debug
@@ -58,7 +58,7 @@ def segment_curvature(segmented_img, objects, label=None):
         # Draw segments one by one to group segment tips together
         finding_tips_img = np.zeros(segmented_img.shape[:2], np.uint8)
         cv2.drawContours(finding_tips_img, objects, i, (255, 255, 255), 1, lineType=8)
-        segment_tips = find_tips(finding_tips_img)
+        segment_tips, _, _ = _find_tips(finding_tips_img)
         tip_objects, _ = _cv2_findcontours(bin_img=segment_tips)
         points = []
 

From cf17f11a200235d788d192245cd8c522e93ff9fb Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Wed, 18 Dec 2024 15:41:05 -0600
Subject: [PATCH 04/36] update more instances of find_tips to use helper

---
 plantcv/plantcv/morphology/segment_euclidean_length.py | 4 ++--
 plantcv/plantcv/morphology/segment_insertion_angle.py  | 9 ++-------
 2 files changed, 4 insertions(+), 9 deletions(-)

diff --git a/plantcv/plantcv/morphology/segment_euclidean_length.py b/plantcv/plantcv/morphology/segment_euclidean_length.py
index dea6d99e5..269106d39 100644
--- a/plantcv/plantcv/morphology/segment_euclidean_length.py
+++ b/plantcv/plantcv/morphology/segment_euclidean_length.py
@@ -8,7 +8,7 @@
 from plantcv.plantcv import color_palette
 from plantcv.plantcv._debug import _debug
 from plantcv.plantcv._helpers import _cv2_findcontours
-from plantcv.plantcv.morphology import find_tips
+from plantcv.plantcv.morphology import _find_tips
 from scipy.spatial.distance import euclidean
 
 
@@ -52,7 +52,7 @@ def segment_euclidean_length(segmented_img, objects, label=None):
         # Draw segments one by one to group segment tips together
         finding_tips_img = np.zeros(segmented_img.shape[:2], np.uint8)
         cv2.drawContours(finding_tips_img, objects, i, (255, 255, 255), 1, lineType=8)
-        segment_tips = find_tips(finding_tips_img)
+        segment_tips, _, _ = _find_tips(finding_tips_img)
         tip_objects, _ = _cv2_findcontours(bin_img=segment_tips)
         points = []
         if not len(tip_objects) == 2:
diff --git a/plantcv/plantcv/morphology/segment_insertion_angle.py b/plantcv/plantcv/morphology/segment_insertion_angle.py
index c0cc6e44a..e375f35fd 100644
--- a/plantcv/plantcv/morphology/segment_insertion_angle.py
+++ b/plantcv/plantcv/morphology/segment_insertion_angle.py
@@ -10,7 +10,7 @@
 from plantcv.plantcv import fatal_error
 from plantcv.plantcv import color_palette
 from plantcv.plantcv.morphology import _iterative_prune
-from plantcv.plantcv.morphology import find_tips
+from plantcv.plantcv.morphology import _find_tips
 from plantcv.plantcv.morphology.segment_tangent_angle import _slope_to_intesect_angle
 from plantcv.plantcv._debug import _debug
 from plantcv.plantcv._helpers import _cv2_findcontours
@@ -62,12 +62,7 @@ def segment_insertion_angle(skel_img, segmented_img, leaf_objects, stem_objects,
     pruned_away = []
 
     # Create a list of tip tuples to use for sorting
-    tips = find_tips(skel_img)
-    tips = dilate(tips, 3, 1)
-    tip_objects, _ = _cv2_findcontours(bin_img=tips)
-    tip_tuples = []
-    for i, cnt in enumerate(tip_objects):
-        tip_tuples.append((cnt[0][0][0], cnt[0][0][1]))
+    tips, tip_tuples, _ = _find_tips(skel_img)
 
     for i, cnt in enumerate(leaf_objects):
         # Draw leaf objects

From 034ebac57f8c8bab53bc3dc9586167ed290c2b7a Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Wed, 18 Dec 2024 15:46:21 -0600
Subject: [PATCH 05/36] remove label from helper function

---
 plantcv/plantcv/morphology/find_tips.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/plantcv/plantcv/morphology/find_tips.py b/plantcv/plantcv/morphology/find_tips.py
index 07791201f..4299e363f 100644
--- a/plantcv/plantcv/morphology/find_tips.py
+++ b/plantcv/plantcv/morphology/find_tips.py
@@ -26,10 +26,6 @@ def _find_tips(skel_img, mask=None):
     :param label: str
     :return tip_img: numpy.ndarray
     """
-    # Set lable to params.sample_label if None
-    if label is None:
-        label = params.sample_label
-
     # In a kernel: 1 values line up with 255s, -1s line up with 0s, and 0s correspond to dont care
     endpoint1 = np.array([[-1, -1, -1],
                           [-1, 1, -1],

From d0f49b204132cb284dddb01343bd63033ddd3d50 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Wed, 18 Dec 2024 15:46:25 -0600
Subject: [PATCH 06/36] Update __init__.py

---
 plantcv/plantcv/morphology/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/plantcv/plantcv/morphology/__init__.py b/plantcv/plantcv/morphology/__init__.py
index 858112df5..df866f756 100644
--- a/plantcv/plantcv/morphology/__init__.py
+++ b/plantcv/plantcv/morphology/__init__.py
@@ -1,5 +1,5 @@
 from plantcv.plantcv.morphology.find_branch_pts import find_branch_pts
-from plantcv.plantcv.morphology.find_tips import find_tips
+from plantcv.plantcv.morphology.find_tips import _find_tips, find_tips
 from plantcv.plantcv.morphology._iterative_prune import _iterative_prune
 from plantcv.plantcv.morphology.segment_skeleton import segment_skeleton
 from plantcv.plantcv.morphology.segment_sort import segment_sort
@@ -17,7 +17,7 @@
 from plantcv.plantcv.morphology.analyze_stem import analyze_stem
 from plantcv.plantcv.morphology.fill_segments import fill_segments
 
-__all__ = ["find_branch_pts", "find_tips", "prune", "skeletonize", "check_cycles", "segment_skeleton", "segment_angle",
+__all__ = ["find_branch_pts", "_find_tips", "find_tips", "prune", "skeletonize", "check_cycles", "segment_skeleton", "segment_angle",
            "segment_path_length", "segment_euclidean_length", "segment_curvature", "segment_sort", "segment_id",
            "segment_tangent_angle", "segment_insertion_angle", "segment_combine", "_iterative_prune", "analyze_stem",
            "fill_segments"]

From 0ea31289b13c80e609775e4f0c8aa1bf4d142deb Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Thu, 19 Dec 2024 09:39:02 -0600
Subject: [PATCH 07/36] add label logic into the front facing function

---
 plantcv/plantcv/morphology/find_tips.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/plantcv/plantcv/morphology/find_tips.py b/plantcv/plantcv/morphology/find_tips.py
index 4299e363f..66c3a24ba 100644
--- a/plantcv/plantcv/morphology/find_tips.py
+++ b/plantcv/plantcv/morphology/find_tips.py
@@ -100,6 +100,10 @@ def find_tips(skel_img, mask=None, label=None):
     tip_img, tip_list, tip_labels = _find_tips(skel_img=skel_img, mask=mask)
 
     _debug(visual=tip_img, filename=os.path.join(params.debug_outdir, f"{params.device}_skeleton_tips.png"))
+    
+    # Set lable to params.sample_label if None
+    if label is None:
+        label = params.sample_label
     # Save coordinates to Outputs 
     outputs.add_observation(sample=label, variable='tips', trait='list of tip coordinates identified from a skeleton',
                             method='plantcv.plantcv.morphology.find_tips', scale='pixels', datatype=list,

From 66f25fbad04589c3e2d6b4d1300a1a4c383ab4ea Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Thu, 19 Dec 2024 09:39:19 -0600
Subject: [PATCH 08/36] update segment sort stop editing tip info

---
 plantcv/plantcv/morphology/segment_sort.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/plantcv/plantcv/morphology/segment_sort.py b/plantcv/plantcv/morphology/segment_sort.py
index c86c4bcde..836eb0225 100644
--- a/plantcv/plantcv/morphology/segment_sort.py
+++ b/plantcv/plantcv/morphology/segment_sort.py
@@ -7,7 +7,7 @@
 from plantcv.plantcv import params
 from plantcv.plantcv import outputs
 from plantcv.plantcv import logical_and
-from plantcv.plantcv.morphology import find_tips
+from plantcv.plantcv.morphology import _find_tips
 from plantcv.plantcv._debug import _debug
 
 
@@ -47,7 +47,7 @@ def segment_sort(skel_img, objects, mask=None, first_stem=True):
     else:
         labeled_img = mask.copy()
 
-    tips_img = find_tips(skel_img)
+    tips_img, _, _ = _find_tips(skel_img)
     tips_img = dilate(tips_img, 3, 1)
 
     # Loop through segment contours
@@ -59,10 +59,6 @@ def segment_sort(skel_img, objects, mask=None, first_stem=True):
         # The first contour is the base, and while it contains a tip, it isn't a leaf
         if i == 0 and first_stem:
             primary_objects.append(cnt)
-            # Remove the first "tip" since it corresponds to stem not leaf. This helps
-            # leaf number to match the number of "tips"
-            outputs.observations[label]["tips"]["value"] = outputs.observations[label]["tips"]["value"][1:]
-            outputs.observations[label]["tips"]["label"] = outputs.observations[label]["tips"]["label"][:-1]
 
         # Sort segments
         else:

From 7558e8c9d288f9fd03d30f34fb43e2077eb5a9ed Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Thu, 19 Dec 2024 11:41:37 -0600
Subject: [PATCH 09/36] add segment_ends to morphology init

---
 plantcv/plantcv/morphology/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/plantcv/plantcv/morphology/__init__.py b/plantcv/plantcv/morphology/__init__.py
index df866f756..1e59eecfd 100644
--- a/plantcv/plantcv/morphology/__init__.py
+++ b/plantcv/plantcv/morphology/__init__.py
@@ -16,8 +16,9 @@
 from plantcv.plantcv.morphology.segment_combine import segment_combine
 from plantcv.plantcv.morphology.analyze_stem import analyze_stem
 from plantcv.plantcv.morphology.fill_segments import fill_segments
+from plantcv.plantcv.morphology.segment_ends import segment_ends
 
 __all__ = ["find_branch_pts", "_find_tips", "find_tips", "prune", "skeletonize", "check_cycles", "segment_skeleton", "segment_angle",
            "segment_path_length", "segment_euclidean_length", "segment_curvature", "segment_sort", "segment_id",
            "segment_tangent_angle", "segment_insertion_angle", "segment_combine", "_iterative_prune", "analyze_stem",
-           "fill_segments"]
+           "fill_segments", "segment_ends"]

From acffd97276e64180409fa8596a408b86edf84565 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Thu, 19 Dec 2024 12:11:03 -0600
Subject: [PATCH 10/36] add segment_img as required input, add outputs

img input not just for plotting debug
---
 plantcv/plantcv/morphology/segment_ends.py | 37 +++++++++++++---------
 1 file changed, 22 insertions(+), 15 deletions(-)

diff --git a/plantcv/plantcv/morphology/segment_ends.py b/plantcv/plantcv/morphology/segment_ends.py
index 9d8ea1da6..9fe83521f 100644
--- a/plantcv/plantcv/morphology/segment_ends.py
+++ b/plantcv/plantcv/morphology/segment_ends.py
@@ -2,40 +2,36 @@
 import os
 import cv2
 import numpy as np
-from plantcv.plantcv import params
+from plantcv.plantcv import params, outputs
 from plantcv.plantcv._debug import _debug
 from plantcv.plantcv.morphology import _iterative_prune
 from plantcv.plantcv._helpers import _cv2_findcontours
 
 
-def segment_ends(objects, mask=None, label=None):
+def segment_ends(segmented_img, objects, label=None):
     """Find tips in skeletonized image.
     The endpoints algorithm was inspired by Jean-Patrick Pommier: https://gist.github.com/jeanpat/5712699
 
     Inputs:
-    skel_img    = Skeletonized image
+    objects     = List of contours to analyze
     mask        = (Optional) binary mask for debugging. If provided, debug image will be overlaid on the mask.
     label       = Optional label parameter, modifies the variable name of
                   observations recorded (default = pcv.params.sample_label).
-    Returns:
-    tip_img   = Image with just tips, rest 0
 
-    :param skel_img: numpy.ndarray
-    :param mask: numpy.ndarray
+    :param segmented_img: numpy.ndarray
+    :param objects: list
     :param label: str
-    :return tip_img: numpy.ndarray
     """
     
-    mask_copy = mask.copy()
+    labeled_img = segmented_img.copy()
     leaf_objects = objects
-    tip_plot = cv2.cvtColor(mask_copy, cv2.COLOR_GRAY2RGB)
     segment_end_objs1 = [] 
     segment_end_objs2 = [] 
 
     # Find segment end coordinates
     for i in range(len(leaf_objects)):
         # Draw leaf objects
-        find_segment_tangents = np.zeros(mask.shape[:2], np.uint8)
+        find_segment_tangents = np.zeros(labeled_img.shape[:2], np.uint8)
         cv2.drawContours(find_segment_tangents, leaf_objects, i, 255, 1, lineType=8)
         # Prune back ends of leaves
         pruned_segment = _iterative_prune(find_segment_tangents, 1)
@@ -55,11 +51,22 @@ def segment_ends(objects, mask=None, label=None):
         inner_list.append(coord)
         print(coord)
         labels.append(i)
-        cv2.drawContours(tip_plot, leaf_objects, i, (150, 150, 150), params.line_thickness, lineType=8)  # segments
-        cv2.circle(tip_plot, (x, y), params.line_thickness, (50, 0, 255), -1)  # Red auricles
+        cv2.drawContours(labeled_img, leaf_objects, i, (150, 150, 150), params.line_thickness, lineType=8)  # segments
+        cv2.circle(labeled_img, (x, y), params.line_thickness, (50, 0, 255), -1)  # Red auricles
         tip = segment_end_objs2[i]
         x, y = tip.ravel()[:2]
         coord = (int(x), int(y))
         tip_list.append(coord)
-        cv2.circle(tip_plot, (x, y), params.line_thickness, (0, 255, 0), -1)  # green tips
-    _debug(visual=tip_plot, filename=os.path.join(params.debug_outdir, f"{params.device}_segment_ends.png"))
+        cv2.circle(labeled_img, (x, y), params.line_thickness, (0, 255, 0), -1)  # green tips
+
+    # Set lable to params.sample_label if None
+    if label is None:
+        label = params.sample_label
+    # Save coordinates to Outputs 
+    outputs.add_observation(sample=label, variable='segment_tips', trait='list of tip coordinates identified from segments',
+                            method='plantcv.plantcv.morphology.segment_ends', scale='None', datatype=list,
+                            value=tip_list, label=labels)
+    outputs.add_observation(sample=label, variable='segment_branch_points', trait='list of branch point coordinates identified from segments',
+                            method='plantcv.plantcv.morphology.segment_ends', scale='None', datatype=list,
+                            value=inner_list, label=labels)
+    _debug(visual=labeled_img, filename=os.path.join(params.debug_outdir, f"{params.device}_segment_ends.png"))

From 43cfbdb2e90e1160f0cbdef2c2449b476d31bafe Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Thu, 19 Dec 2024 12:11:19 -0600
Subject: [PATCH 11/36] Create test_segment_ends.py

---
 tests/plantcv/morphology/test_segment_ends.py | 11 +++++++++++
 1 file changed, 11 insertions(+)
 create mode 100644 tests/plantcv/morphology/test_segment_ends.py

diff --git a/tests/plantcv/morphology/test_segment_ends.py b/tests/plantcv/morphology/test_segment_ends.py
new file mode 100644
index 000000000..970fca890
--- /dev/null
+++ b/tests/plantcv/morphology/test_segment_ends.py
@@ -0,0 +1,11 @@
+import cv2
+from plantcv.plantcv import outputs
+from plantcv.plantcv.morphology import segment_ends
+
+
+def test_segment_ends(morphology_test_data):
+    """Test for PlantCV."""
+    leaf_obj = morphology_test_data.load_segments(morphology_test_data.segments_file, "leaves")
+    skeleton = cv2.imread(morphology_test_data.skel_img, -1)
+    segment_ends(segmented_img=skeleton, objects=leaf_obj)
+    assert len(outputs.observations['default']['segment_branch_points']['value']) == 4

From 81d05747aac19bb2243beb6d71be4889411c7b83 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Thu, 19 Dec 2024 12:18:05 -0600
Subject: [PATCH 12/36] update segment_id allow optimal_assignment of IDs

---
 plantcv/plantcv/morphology/segment_id.py | 24 +++++++++++++++++++-----
 1 file changed, 19 insertions(+), 5 deletions(-)

diff --git a/plantcv/plantcv/morphology/segment_id.py b/plantcv/plantcv/morphology/segment_id.py
index bf24db742..a7277772d 100644
--- a/plantcv/plantcv/morphology/segment_id.py
+++ b/plantcv/plantcv/morphology/segment_id.py
@@ -7,13 +7,14 @@
 from plantcv.plantcv._debug import _debug
 
 
-def segment_id(skel_img, objects, mask=None):
+def segment_id(skel_img, objects, mask=None, optimal_assignment=None):
     """Plot segment IDs.
 
     Inputs:
     skel_img      = Skeletonized image
     objects       = List of contours
     mask          = (Optional) binary mask for debugging. If provided, debug image will be overlaid on the mask.
+    optimal_assignment = functions similar to the "label" parameter where it replaces the unique labels 
 
     Returns:
     segmented_img = Segmented image
@@ -38,9 +39,14 @@ def segment_id(skel_img, objects, mask=None):
     # Create a color scale, use a previously stored scale if available
     rand_color = color_palette(num=len(objects), saved=True)
 
+    
     # Plot all segment contours
     for i, cnt in enumerate(objects):
-        cv2.drawContours(segmented_img, cnt, -1, rand_color[i], params.line_thickness, lineType=8)
+        if optimal_assignment is not None:
+            color_index = optimal_assignment[i]
+        else: 
+            color_index = i
+        cv2.drawContours(segmented_img, cnt, -1, rand_color[color_index], params.line_thickness, lineType=8)
         # Store coordinates for labels
         label_coord_x.append(objects[i][0][0][0])
         label_coord_y.append(objects[i][0][0][1])
@@ -48,12 +54,20 @@ def segment_id(skel_img, objects, mask=None):
     labeled_img = segmented_img.copy()
 
     for i, cnt in enumerate(objects):
-        # Label slope lines
+        if optimal_assignment is not None:
+            # relabel IDs
+            text = f"{optimal_assignment[i]}"
+            color_index = optimal_assignment[i]
+
+        else:
+            text = f"{i}"
+            color_index = i
+        # Label segments
         w = label_coord_x[i]
         h = label_coord_y[i]
-        text = f"ID:{i}"
+        
         cv2.putText(img=labeled_img, text=text, org=(w, h), fontFace=cv2.FONT_HERSHEY_SIMPLEX,
-                    fontScale=params.text_size, color=rand_color[i], thickness=params.text_thickness)
+                    fontScale=params.text_size, color=rand_color[color_index], thickness=params.text_thickness)
 
     _debug(visual=labeled_img, filename=os.path.join(params.debug_outdir, f"{params.device}_segmented_ids.png"))
 

From 4c48eacef6c442c3a332a72e4e4ced556309df36 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Thu, 19 Dec 2024 13:39:20 -0600
Subject: [PATCH 13/36] Update test_segment_id.py

add optimal assignment input
---
 tests/plantcv/morphology/test_segment_id.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/plantcv/morphology/test_segment_id.py b/tests/plantcv/morphology/test_segment_id.py
index bed778194..256f47dc2 100644
--- a/tests/plantcv/morphology/test_segment_id.py
+++ b/tests/plantcv/morphology/test_segment_id.py
@@ -6,7 +6,7 @@ def test_segment_id(morphology_test_data):
     """Test for PlantCV."""
     skel = cv2.imread(morphology_test_data.skel_img, -1)
     leaf_obj = morphology_test_data.load_segments(morphology_test_data.segments_file, "leaves")
-    _, labeled_img = segment_id(skel_img=skel, objects=leaf_obj, mask=skel)
+    _, labeled_img = segment_id(skel_img=skel, objects=leaf_obj, mask=skel, optimal_assignment=[0,1,2,3])
     assert skel.shape == labeled_img.shape[:2]
 
 

From eddfab50e46f80784f35230448df46065e0a97f6 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Fri, 20 Dec 2024 10:59:47 -0600
Subject: [PATCH 14/36] convert to color for debug image

---
 plantcv/plantcv/morphology/segment_ends.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/plantcv/plantcv/morphology/segment_ends.py b/plantcv/plantcv/morphology/segment_ends.py
index 9fe83521f..5de05eb74 100644
--- a/plantcv/plantcv/morphology/segment_ends.py
+++ b/plantcv/plantcv/morphology/segment_ends.py
@@ -24,6 +24,8 @@ def segment_ends(segmented_img, objects, label=None):
     """
     
     labeled_img = segmented_img.copy()
+    if len(np.shape(labeled_img)) == 2:
+        labeled_img = cv2.cvtColor(labeled_img, cv2.COLOR_GRAY2RGB)
     leaf_objects = objects
     segment_end_objs1 = [] 
     segment_end_objs2 = [] 

From 49bdc7835eff0a4a43383cca09303777770c31a6 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Fri, 20 Dec 2024 14:00:10 -0600
Subject: [PATCH 15/36] segment_ends check tip or branch_pt

---
 plantcv/plantcv/morphology/segment_ends.py | 76 ++++++++++++----------
 1 file changed, 42 insertions(+), 34 deletions(-)

diff --git a/plantcv/plantcv/morphology/segment_ends.py b/plantcv/plantcv/morphology/segment_ends.py
index 5de05eb74..1567d9868 100644
--- a/plantcv/plantcv/morphology/segment_ends.py
+++ b/plantcv/plantcv/morphology/segment_ends.py
@@ -2,65 +2,71 @@
 import os
 import cv2
 import numpy as np
+from plantcv.plantcv import dilate, logical_and
 from plantcv.plantcv import params, outputs
 from plantcv.plantcv._debug import _debug
-from plantcv.plantcv.morphology import _iterative_prune
+from plantcv.plantcv.morphology import _iterative_prune, _find_tips
 from plantcv.plantcv._helpers import _cv2_findcontours
 
 
-def segment_ends(segmented_img, objects, label=None):
-    """Find tips in skeletonized image.
-    The endpoints algorithm was inspired by Jean-Patrick Pommier: https://gist.github.com/jeanpat/5712699
+def segment_ends(skel_img, leaf_objects, mask=None, label=None):
+    """Find tips and segment branch points .
 
     Inputs:
-    objects     = List of contours to analyze
-    mask        = (Optional) binary mask for debugging. If provided, debug image will be overlaid on the mask.
-    label       = Optional label parameter, modifies the variable name of
-                  observations recorded (default = pcv.params.sample_label).
+    skel_img         = Skeletonized image
+    leaf_objects     = List of leaf segments
+    mask             = (Optional) binary mask for debugging. If provided, debug image will be overlaid on the mask.
+    label            = Optional label parameter, modifies the variable name of
+                       observations recorded (default = pcv.params.sample_label).
 
     :param segmented_img: numpy.ndarray
     :param objects: list
     :param label: str
     """
+    # Store debug
+    debug = params.debug
+    params.debug = None
     
-    labeled_img = segmented_img.copy()
-    if len(np.shape(labeled_img)) == 2:
-        labeled_img = cv2.cvtColor(labeled_img, cv2.COLOR_GRAY2RGB)
-    leaf_objects = objects
-    segment_end_objs1 = [] 
-    segment_end_objs2 = [] 
+    
+    if mask is None:
+        labeled_img = skel_img.copy()
+    else:
+        labeled_img = mask.copy()
+    labeled_img = cv2.cvtColor(labeled_img, cv2.COLOR_GRAY2RGB)
+    tips, _, _ = _find_tips(skel_img)
+    # Initialize list of tip data points
+    tip_list = []
+    labels = []
+    inner_list = [] 
 
     # Find segment end coordinates
     for i in range(len(leaf_objects)):
+        labels.append(i)
         # Draw leaf objects
         find_segment_tangents = np.zeros(labeled_img.shape[:2], np.uint8)
         cv2.drawContours(find_segment_tangents, leaf_objects, i, 255, 1, lineType=8)
+        cv2.drawContours(labeled_img, leaf_objects, i, (150, 150, 150), params.line_thickness, lineType=8)  # segments debug
         # Prune back ends of leaves
         pruned_segment = _iterative_prune(find_segment_tangents, 1)
         # Segment ends are the portions pruned off
         segment_ends = find_segment_tangents - pruned_segment
         segment_end_obj, _ = _cv2_findcontours(bin_img=segment_ends)
-        segment_end_objs1.append(segment_end_obj[0])
-        segment_end_objs2.append(segment_end_obj[1])
-        
-    # Initialize list of tip data points
-    tip_list = []
-    labels = []
-    inner_list = [] 
-    for i, coor in enumerate(segment_end_objs1):
-        x, y = coor.ravel()[:2]
-        coord = (int(x), int(y))
-        inner_list.append(coord)
-        print(coord)
-        labels.append(i)
-        cv2.drawContours(labeled_img, leaf_objects, i, (150, 150, 150), params.line_thickness, lineType=8)  # segments
-        cv2.circle(labeled_img, (x, y), params.line_thickness, (50, 0, 255), -1)  # Red auricles
-        tip = segment_end_objs2[i]
-        x, y = tip.ravel()[:2]
-        coord = (int(x), int(y))
-        tip_list.append(coord)
-        cv2.circle(labeled_img, (x, y), params.line_thickness, (0, 255, 0), -1)  # green tips
+        # Determine if a segment is segment tip or branch point
+        for j, obj in enumerate(segment_end_obj):
+            segment_plot = np.zeros(skel_img.shape[:2], np.uint8)
+            cv2.drawContours(segment_plot, obj, -1, 255, 1, lineType=8)
+            segment_plot = dilate(segment_plot, 3, 1)
+            overlap_img = logical_and(segment_plot, tips)
+            x, y = segment_end_obj[j].ravel()[:2]
+            coord = (int(x), int(y))
 
+            # If none of the tips are within a segment_end then it's an insertion segment
+            if np.sum(overlap_img) == 0:
+                inner_list.append(coord)
+                cv2.circle(labeled_img, coord, params.line_thickness, (50, 0, 255), -1)  # Red auricles
+            else:
+                tip_list.append(coord)
+                cv2.circle(labeled_img, coord, params.line_thickness, (0, 255, 0), -1)  # green tips
     # Set lable to params.sample_label if None
     if label is None:
         label = params.sample_label
@@ -71,4 +77,6 @@ def segment_ends(segmented_img, objects, label=None):
     outputs.add_observation(sample=label, variable='segment_branch_points', trait='list of branch point coordinates identified from segments',
                             method='plantcv.plantcv.morphology.segment_ends', scale='None', datatype=list,
                             value=inner_list, label=labels)
+    # Reset debug mode
+    params.debug = debug
     _debug(visual=labeled_img, filename=os.path.join(params.debug_outdir, f"{params.device}_segment_ends.png"))

From 5753678d964cf9a47a320127fe8aa0a5625f63ae Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Mon, 23 Dec 2024 09:10:39 -0600
Subject: [PATCH 16/36] test_segment_ends_no_mask

---
 tests/plantcv/morphology/test_segment_ends.py | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/tests/plantcv/morphology/test_segment_ends.py b/tests/plantcv/morphology/test_segment_ends.py
index 970fca890..e3a05e84c 100644
--- a/tests/plantcv/morphology/test_segment_ends.py
+++ b/tests/plantcv/morphology/test_segment_ends.py
@@ -5,7 +5,19 @@
 
 def test_segment_ends(morphology_test_data):
     """Test for PlantCV."""
+    # Clear previous outputs
+    outputs.clear()
     leaf_obj = morphology_test_data.load_segments(morphology_test_data.segments_file, "leaves")
     skeleton = cv2.imread(morphology_test_data.skel_img, -1)
-    segment_ends(segmented_img=skeleton, objects=leaf_obj)
+    segment_ends(skel_img=skeleton, leaf_objects=leaf_obj, mask=skeleton)
     assert len(outputs.observations['default']['segment_branch_points']['value']) == 4
+
+
+def test_segment_ends_no_mask(morphology_test_data):
+    """Test for PlantCV."""
+    # Clear previous outputs
+    outputs.clear()
+    leaf_obj = morphology_test_data.load_segments(morphology_test_data.segments_file, "leaves")
+    skeleton = cv2.imread(morphology_test_data.skel_img, -1)
+    segment_ends(skel_img=skeleton, leaf_objects=leaf_obj, mask=None)
+    assert len(outputs.observations['default']['segment_branch_points']['value']) == 4
\ No newline at end of file

From fc6074d1d543268ef69e89e320150d5fafeed0ae Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Mon, 23 Dec 2024 09:13:54 -0600
Subject: [PATCH 17/36] segment_sort no need to store label

since no outputs in sorting, skip the label storage. wasn't used downstream but also don't need to store anymore since _find_tips also doesn't store to outputs
---
 plantcv/plantcv/morphology/segment_sort.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/plantcv/plantcv/morphology/segment_sort.py b/plantcv/plantcv/morphology/segment_sort.py
index 836eb0225..152f99884 100644
--- a/plantcv/plantcv/morphology/segment_sort.py
+++ b/plantcv/plantcv/morphology/segment_sort.py
@@ -5,7 +5,6 @@
 import numpy as np
 from plantcv.plantcv import dilate
 from plantcv.plantcv import params
-from plantcv.plantcv import outputs
 from plantcv.plantcv import logical_and
 from plantcv.plantcv.morphology import _find_tips
 from plantcv.plantcv._debug import _debug
@@ -36,9 +35,6 @@ def segment_sort(skel_img, objects, mask=None, first_stem=True):
     debug = params.debug
     params.debug = None
 
-    # Store label
-    label = params.sample_label
-
     secondary_objects = []
     primary_objects = []
 

From be3cdb7e412439d71776f4bc3943b71966a9491d Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Mon, 23 Dec 2024 09:36:03 -0600
Subject: [PATCH 18/36] Re-defined variable from outer scope

---
 plantcv/plantcv/morphology/segment_ends.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/plantcv/plantcv/morphology/segment_ends.py b/plantcv/plantcv/morphology/segment_ends.py
index 1567d9868..3a04b53d0 100644
--- a/plantcv/plantcv/morphology/segment_ends.py
+++ b/plantcv/plantcv/morphology/segment_ends.py
@@ -49,8 +49,8 @@ def segment_ends(skel_img, leaf_objects, mask=None, label=None):
         # Prune back ends of leaves
         pruned_segment = _iterative_prune(find_segment_tangents, 1)
         # Segment ends are the portions pruned off
-        segment_ends = find_segment_tangents - pruned_segment
-        segment_end_obj, _ = _cv2_findcontours(bin_img=segment_ends)
+        ends = find_segment_tangents - pruned_segment
+        segment_end_obj, _ = _cv2_findcontours(bin_img=ends)
         # Determine if a segment is segment tip or branch point
         for j, obj in enumerate(segment_end_obj):
             segment_plot = np.zeros(skel_img.shape[:2], np.uint8)

From 86db239bc959bbc05084c378c34fb1aeed383720 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Mon, 23 Dec 2024 09:36:13 -0600
Subject: [PATCH 19/36] remove unused var

---
 plantcv/plantcv/morphology/segment_insertion_angle.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plantcv/plantcv/morphology/segment_insertion_angle.py b/plantcv/plantcv/morphology/segment_insertion_angle.py
index e375f35fd..9c84ce570 100644
--- a/plantcv/plantcv/morphology/segment_insertion_angle.py
+++ b/plantcv/plantcv/morphology/segment_insertion_angle.py
@@ -62,7 +62,7 @@ def segment_insertion_angle(skel_img, segmented_img, leaf_objects, stem_objects,
     pruned_away = []
 
     # Create a list of tip tuples to use for sorting
-    tips, tip_tuples, _ = _find_tips(skel_img)
+    tips, _, _ = _find_tips(skel_img)
 
     for i, cnt in enumerate(leaf_objects):
         # Draw leaf objects

From 9e84adcb3f0df5d7df32470b0c5effbdad9d4286 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Mon, 23 Dec 2024 09:37:24 -0600
Subject: [PATCH 20/36] white space fixes

---
 plantcv/plantcv/morphology/find_tips.py  | 1 +
 plantcv/plantcv/morphology/segment_id.py | 3 ---
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/plantcv/plantcv/morphology/find_tips.py b/plantcv/plantcv/morphology/find_tips.py
index 66c3a24ba..e565bb6b9 100644
--- a/plantcv/plantcv/morphology/find_tips.py
+++ b/plantcv/plantcv/morphology/find_tips.py
@@ -80,6 +80,7 @@ def _find_tips(skel_img, mask=None):
 
     return tip_img, tip_list, tip_labels
 
+
 def find_tips(skel_img, mask=None, label=None):
     """Find tips in skeletonized image.
     The endpoints algorithm was inspired by Jean-Patrick Pommier: https://gist.github.com/jeanpat/5712699
diff --git a/plantcv/plantcv/morphology/segment_id.py b/plantcv/plantcv/morphology/segment_id.py
index a7277772d..f2f5a5869 100644
--- a/plantcv/plantcv/morphology/segment_id.py
+++ b/plantcv/plantcv/morphology/segment_id.py
@@ -39,7 +39,6 @@ def segment_id(skel_img, objects, mask=None, optimal_assignment=None):
     # Create a color scale, use a previously stored scale if available
     rand_color = color_palette(num=len(objects), saved=True)
 
-    
     # Plot all segment contours
     for i, cnt in enumerate(objects):
         if optimal_assignment is not None:
@@ -58,14 +57,12 @@ def segment_id(skel_img, objects, mask=None, optimal_assignment=None):
             # relabel IDs
             text = f"{optimal_assignment[i]}"
             color_index = optimal_assignment[i]
-
         else:
             text = f"{i}"
             color_index = i
         # Label segments
         w = label_coord_x[i]
         h = label_coord_y[i]
-        
         cv2.putText(img=labeled_img, text=text, org=(w, h), fontFace=cv2.FONT_HERSHEY_SIMPLEX,
                     fontScale=params.text_size, color=rand_color[color_index], thickness=params.text_thickness)
 

From dcea2a9e877b2ba17c2d1cebb2335fb4fd1a1bbc Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Mon, 23 Dec 2024 09:38:28 -0600
Subject: [PATCH 21/36] line length fixes

---
 plantcv/plantcv/morphology/__init__.py     | 3 ++-
 plantcv/plantcv/morphology/segment_ends.py | 6 ++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/plantcv/plantcv/morphology/__init__.py b/plantcv/plantcv/morphology/__init__.py
index 1e59eecfd..04fe24db3 100644
--- a/plantcv/plantcv/morphology/__init__.py
+++ b/plantcv/plantcv/morphology/__init__.py
@@ -18,7 +18,8 @@
 from plantcv.plantcv.morphology.fill_segments import fill_segments
 from plantcv.plantcv.morphology.segment_ends import segment_ends
 
-__all__ = ["find_branch_pts", "_find_tips", "find_tips", "prune", "skeletonize", "check_cycles", "segment_skeleton", "segment_angle",
+__all__ = ["find_branch_pts", "_find_tips", "find_tips", "prune", "skeletonize", "check_cycles",
+           "segment_skeleton", "segment_angle",
            "segment_path_length", "segment_euclidean_length", "segment_curvature", "segment_sort", "segment_id",
            "segment_tangent_angle", "segment_insertion_angle", "segment_combine", "_iterative_prune", "analyze_stem",
            "fill_segments", "segment_ends"]
diff --git a/plantcv/plantcv/morphology/segment_ends.py b/plantcv/plantcv/morphology/segment_ends.py
index 3a04b53d0..6792258dc 100644
--- a/plantcv/plantcv/morphology/segment_ends.py
+++ b/plantcv/plantcv/morphology/segment_ends.py
@@ -71,10 +71,12 @@ def segment_ends(skel_img, leaf_objects, mask=None, label=None):
     if label is None:
         label = params.sample_label
     # Save coordinates to Outputs 
-    outputs.add_observation(sample=label, variable='segment_tips', trait='list of tip coordinates identified from segments',
+    outputs.add_observation(sample=label, variable='segment_tips',
+                            trait='list of tip coordinates identified from segments',
                             method='plantcv.plantcv.morphology.segment_ends', scale='None', datatype=list,
                             value=tip_list, label=labels)
-    outputs.add_observation(sample=label, variable='segment_branch_points', trait='list of branch point coordinates identified from segments',
+    outputs.add_observation(sample=label, variable='segment_branch_points',
+                            trait='list of branch point coordinates identified from segments',
                             method='plantcv.plantcv.morphology.segment_ends', scale='None', datatype=list,
                             value=inner_list, label=labels)
     # Reset debug mode

From 333e3539c21e6b096b271d792cd35af97a337d9f Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Mon, 23 Dec 2024 09:40:49 -0600
Subject: [PATCH 22/36] remove trailing whitespace

---
 plantcv/plantcv/morphology/find_tips.py    | 2 +-
 plantcv/plantcv/morphology/segment_ends.py | 6 +++---
 plantcv/plantcv/morphology/segment_id.py   | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/plantcv/plantcv/morphology/find_tips.py b/plantcv/plantcv/morphology/find_tips.py
index e565bb6b9..c8a045f37 100644
--- a/plantcv/plantcv/morphology/find_tips.py
+++ b/plantcv/plantcv/morphology/find_tips.py
@@ -105,7 +105,7 @@ def find_tips(skel_img, mask=None, label=None):
     # Set lable to params.sample_label if None
     if label is None:
         label = params.sample_label
-    # Save coordinates to Outputs 
+    # Save coordinates to Outputs
     outputs.add_observation(sample=label, variable='tips', trait='list of tip coordinates identified from a skeleton',
                             method='plantcv.plantcv.morphology.find_tips', scale='pixels', datatype=list,
                             value=tip_list, label=tip_labels)
diff --git a/plantcv/plantcv/morphology/segment_ends.py b/plantcv/plantcv/morphology/segment_ends.py
index 6792258dc..b072d1de2 100644
--- a/plantcv/plantcv/morphology/segment_ends.py
+++ b/plantcv/plantcv/morphology/segment_ends.py
@@ -1,4 +1,4 @@
-# Find both segment end coordinates 
+# Find both segment end coordinates
 import os
 import cv2
 import numpy as np
@@ -37,7 +37,7 @@ def segment_ends(skel_img, leaf_objects, mask=None, label=None):
     # Initialize list of tip data points
     tip_list = []
     labels = []
-    inner_list = [] 
+    inner_list = []
 
     # Find segment end coordinates
     for i in range(len(leaf_objects)):
@@ -70,7 +70,7 @@ def segment_ends(skel_img, leaf_objects, mask=None, label=None):
     # Set lable to params.sample_label if None
     if label is None:
         label = params.sample_label
-    # Save coordinates to Outputs 
+    # Save coordinates to Outputs
     outputs.add_observation(sample=label, variable='segment_tips',
                             trait='list of tip coordinates identified from segments',
                             method='plantcv.plantcv.morphology.segment_ends', scale='None', datatype=list,
diff --git a/plantcv/plantcv/morphology/segment_id.py b/plantcv/plantcv/morphology/segment_id.py
index f2f5a5869..a1a89e109 100644
--- a/plantcv/plantcv/morphology/segment_id.py
+++ b/plantcv/plantcv/morphology/segment_id.py
@@ -14,7 +14,7 @@ def segment_id(skel_img, objects, mask=None, optimal_assignment=None):
     skel_img      = Skeletonized image
     objects       = List of contours
     mask          = (Optional) binary mask for debugging. If provided, debug image will be overlaid on the mask.
-    optimal_assignment = functions similar to the "label" parameter where it replaces the unique labels 
+    optimal_assignment = functions similar to the "label" parameter where it replaces the unique labels
 
     Returns:
     segmented_img = Segmented image
@@ -43,7 +43,7 @@ def segment_id(skel_img, objects, mask=None, optimal_assignment=None):
     for i, cnt in enumerate(objects):
         if optimal_assignment is not None:
             color_index = optimal_assignment[i]
-        else: 
+        else:
             color_index = i
         cv2.drawContours(segmented_img, cnt, -1, rand_color[color_index], params.line_thickness, lineType=8)
         # Store coordinates for labels

From ee3e4be9adb9f6b080d3bb0acf036dfabe05985b Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Mon, 23 Dec 2024 10:58:55 -0600
Subject: [PATCH 23/36] more whitespaces fixes

---
 plantcv/plantcv/morphology/find_tips.py    | 4 ++--
 plantcv/plantcv/morphology/segment_ends.py | 4 +---
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/plantcv/plantcv/morphology/find_tips.py b/plantcv/plantcv/morphology/find_tips.py
index c8a045f37..efd396ddd 100644
--- a/plantcv/plantcv/morphology/find_tips.py
+++ b/plantcv/plantcv/morphology/find_tips.py
@@ -109,5 +109,5 @@ def find_tips(skel_img, mask=None, label=None):
     outputs.add_observation(sample=label, variable='tips', trait='list of tip coordinates identified from a skeleton',
                             method='plantcv.plantcv.morphology.find_tips', scale='pixels', datatype=list,
                             value=tip_list, label=tip_labels)
-    
-    return tip_img
\ No newline at end of file
+
+    return tip_img
diff --git a/plantcv/plantcv/morphology/segment_ends.py b/plantcv/plantcv/morphology/segment_ends.py
index b072d1de2..0d9bcf27a 100644
--- a/plantcv/plantcv/morphology/segment_ends.py
+++ b/plantcv/plantcv/morphology/segment_ends.py
@@ -26,8 +26,7 @@ def segment_ends(skel_img, leaf_objects, mask=None, label=None):
     # Store debug
     debug = params.debug
     params.debug = None
-    
-    
+
     if mask is None:
         labeled_img = skel_img.copy()
     else:
@@ -59,7 +58,6 @@ def segment_ends(skel_img, leaf_objects, mask=None, label=None):
             overlap_img = logical_and(segment_plot, tips)
             x, y = segment_end_obj[j].ravel()[:2]
             coord = (int(x), int(y))
-
             # If none of the tips are within a segment_end then it's an insertion segment
             if np.sum(overlap_img) == 0:
                 inner_list.append(coord)

From 0b63217b949c7364d5f6d43221d55e9bea82b8fc Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Mon, 23 Dec 2024 16:31:01 -0600
Subject: [PATCH 24/36] move _iterative_prune and _find_tips to _helpers

rearrage ome imports and change where things are getting called from
---
 plantcv/plantcv/_helpers.py                   | 114 ++++++++++++++++++
 plantcv/plantcv/morphology/__init__.py        |   7 +-
 .../plantcv/morphology/_iterative_prune.py    |  46 -------
 plantcv/plantcv/morphology/find_tips.py       |  77 +-----------
 plantcv/plantcv/morphology/prune.py           |   6 +-
 .../plantcv/morphology/segment_curvature.py   |   3 +-
 plantcv/plantcv/morphology/segment_ends.py    |   4 +-
 .../morphology/segment_euclidean_length.py    |   3 +-
 .../morphology/segment_insertion_angle.py     |   4 +-
 plantcv/plantcv/morphology/segment_sort.py    |   2 +-
 .../morphology/segment_tangent_angle.py       |   3 +-
 tests/plantcv/morphology/test_prune.py        |   9 +-
 12 files changed, 127 insertions(+), 151 deletions(-)
 delete mode 100644 plantcv/plantcv/morphology/_iterative_prune.py

diff --git a/plantcv/plantcv/_helpers.py b/plantcv/plantcv/_helpers.py
index 9b10d7ba0..47a60bb01 100644
--- a/plantcv/plantcv/_helpers.py
+++ b/plantcv/plantcv/_helpers.py
@@ -1,11 +1,125 @@
 import cv2
 import numpy as np
+from plantcv.plantcv.dilate import dilate
 from plantcv.plantcv.logical_and import logical_and
+from plantcv.plantcv.image_subtract import image_subtract
 from plantcv.plantcv import fatal_error, warn
 from plantcv.plantcv import params
 import pandas as pd
 
 
+def _iterative_prune(skel_img, size):
+    """Iteratively remove endpoints (tips) from a skeletonized image.
+    The pruning algorithm was inspired by Jean-Patrick Pommier: https://gist.github.com/jeanpat/5712699
+    "Prunes" barbs off a skeleton.
+    Inputs:
+    skel_img    = Skeletonized image
+    size        = Size to get pruned off each branch
+    Returns:
+    pruned_img  = Pruned image
+    :param skel_img: numpy.ndarray
+    :param size: int
+    :return pruned_img: numpy.ndarray
+    """
+    pruned_img = skel_img.copy()
+    # Store debug
+    debug = params.debug
+    params.debug = None
+
+    # Iteratively remove endpoints (tips) from a skeleton
+    for _ in range(0, size):
+        endpoints, _, _ = _find_tips(pruned_img)
+        pruned_img = image_subtract(pruned_img, endpoints)
+
+    # Make debugging image
+    pruned_plot = np.zeros(skel_img.shape[:2], np.uint8)
+    pruned_plot = cv2.cvtColor(pruned_plot, cv2.COLOR_GRAY2RGB)
+    skel_obj, skel_hierarchy = _cv2_findcontours(bin_img=pruned_img)
+    pruned_obj, pruned_hierarchy = _cv2_findcontours(bin_img=pruned_img)
+
+    # Reset debug mode
+    params.debug = debug
+
+    cv2.drawContours(pruned_plot, skel_obj, -1, (0, 0, 255), params.line_thickness,
+                     lineType=8, hierarchy=skel_hierarchy)
+    cv2.drawContours(pruned_plot, pruned_obj, -1, (255, 255, 255), params.line_thickness,
+                     lineType=8, hierarchy=pruned_hierarchy)
+
+    return pruned_img
+
+
+def _find_tips(skel_img, mask=None):
+    """Helper function to find tips in skeletonized image.
+    The endpoints algorithm was inspired by Jean-Patrick Pommier: https://gist.github.com/jeanpat/5712699
+
+    Inputs:
+    skel_img    = Skeletonized image
+    mask        = (Optional) binary mask for debugging. If provided, debug image will be overlaid on the mask.
+    label       = Optional label parameter, modifies the variable name of
+                  observations recorded (default = pcv.params.sample_label).
+    Returns:
+    tip_img   = Image with just tips, rest 0
+
+    :param skel_img: numpy.ndarray
+    :param mask: numpy.ndarray
+    :param label: str
+    :return tip_img: numpy.ndarray
+    """
+    # In a kernel: 1 values line up with 255s, -1s line up with 0s, and 0s correspond to dont care
+    endpoint1 = np.array([[-1, -1, -1],
+                          [-1, 1, -1],
+                          [0, 1,  0]])
+    endpoint2 = np.array([[-1, -1, -1],
+                          [-1, 1, 0],
+                          [-1, 0, 1]])
+
+    endpoint3 = np.rot90(endpoint1)
+    endpoint4 = np.rot90(endpoint2)
+    endpoint5 = np.rot90(endpoint3)
+    endpoint6 = np.rot90(endpoint4)
+    endpoint7 = np.rot90(endpoint5)
+    endpoint8 = np.rot90(endpoint6)
+
+    endpoints = [endpoint1, endpoint2, endpoint3, endpoint4, endpoint5, endpoint6, endpoint7, endpoint8]
+    tip_img = np.zeros(skel_img.shape[:2], dtype=int)
+    for endpoint in endpoints:
+        tip_img = np.logical_or(cv2.morphologyEx(skel_img, op=cv2.MORPH_HITMISS, kernel=endpoint,
+                                                 borderType=cv2.BORDER_CONSTANT, borderValue=0), tip_img)
+    tip_img = tip_img.astype(np.uint8) * 255
+    # Store debug
+    debug = params.debug
+    params.debug = None
+    tip_objects, _ = _cv2_findcontours(bin_img=tip_img)
+
+    if mask is None:
+        # Make debugging image
+        dilated_skel = dilate(skel_img, params.line_thickness, 1)
+        tip_plot = cv2.cvtColor(dilated_skel, cv2.COLOR_GRAY2RGB)
+
+    else:
+        # Make debugging image on mask
+        mask_copy = mask.copy()
+        tip_plot = cv2.cvtColor(mask_copy, cv2.COLOR_GRAY2RGB)
+        skel_obj, skel_hier = _cv2_findcontours(bin_img=skel_img)
+        cv2.drawContours(tip_plot, skel_obj, -1, (150, 150, 150), params.line_thickness,
+                         lineType=8, hierarchy=skel_hier)
+
+    # Initialize list of tip data points
+    tip_list = []
+    tip_labels = []
+    for i, tip in enumerate(tip_objects):
+        x, y = tip.ravel()[:2]
+        coord = (int(x), int(y))
+        tip_list.append(coord)
+        tip_labels.append(i)
+        cv2.circle(tip_plot, (x, y), params.line_thickness, (0, 255, 0), -1)
+
+    # Reset debug mode
+    params.debug = debug
+
+    return tip_img, tip_list, tip_labels
+
+
 def _hough_circle(gray_img, mindist, candec, accthresh, minradius, maxradius, maxfound=None):
     """
     Hough Circle Detection
diff --git a/plantcv/plantcv/morphology/__init__.py b/plantcv/plantcv/morphology/__init__.py
index 04fe24db3..dc44af6c8 100644
--- a/plantcv/plantcv/morphology/__init__.py
+++ b/plantcv/plantcv/morphology/__init__.py
@@ -1,6 +1,5 @@
 from plantcv.plantcv.morphology.find_branch_pts import find_branch_pts
-from plantcv.plantcv.morphology.find_tips import _find_tips, find_tips
-from plantcv.plantcv.morphology._iterative_prune import _iterative_prune
+from plantcv.plantcv.morphology.find_tips import find_tips
 from plantcv.plantcv.morphology.segment_skeleton import segment_skeleton
 from plantcv.plantcv.morphology.segment_sort import segment_sort
 from plantcv.plantcv.morphology.prune import prune
@@ -18,8 +17,8 @@
 from plantcv.plantcv.morphology.fill_segments import fill_segments
 from plantcv.plantcv.morphology.segment_ends import segment_ends
 
-__all__ = ["find_branch_pts", "_find_tips", "find_tips", "prune", "skeletonize", "check_cycles",
+__all__ = ["find_branch_pts", "find_tips", "prune", "skeletonize", "check_cycles",
            "segment_skeleton", "segment_angle",
            "segment_path_length", "segment_euclidean_length", "segment_curvature", "segment_sort", "segment_id",
-           "segment_tangent_angle", "segment_insertion_angle", "segment_combine", "_iterative_prune", "analyze_stem",
+           "segment_tangent_angle", "segment_insertion_angle", "segment_combine", "analyze_stem",
            "fill_segments", "segment_ends"]
diff --git a/plantcv/plantcv/morphology/_iterative_prune.py b/plantcv/plantcv/morphology/_iterative_prune.py
deleted file mode 100644
index e1f51e128..000000000
--- a/plantcv/plantcv/morphology/_iterative_prune.py
+++ /dev/null
@@ -1,46 +0,0 @@
-import cv2
-import numpy as np
-from plantcv.plantcv import params
-from plantcv.plantcv import image_subtract
-from plantcv.plantcv.morphology import _find_tips
-from plantcv.plantcv._helpers import _cv2_findcontours
-
-
-def _iterative_prune(skel_img, size):
-    """Iteratively remove endpoints (tips) from a skeletonized image.
-    The pruning algorithm was inspired by Jean-Patrick Pommier: https://gist.github.com/jeanpat/5712699
-    "Prunes" barbs off a skeleton.
-    Inputs:
-    skel_img    = Skeletonized image
-    size        = Size to get pruned off each branch
-    Returns:
-    pruned_img  = Pruned image
-    :param skel_img: numpy.ndarray
-    :param size: int
-    :return pruned_img: numpy.ndarray
-    """
-    pruned_img = skel_img.copy()
-    # Store debug
-    debug = params.debug
-    params.debug = None
-
-    # Iteratively remove endpoints (tips) from a skeleton
-    for _ in range(0, size):
-        endpoints, _, _ = _find_tips(pruned_img)
-        pruned_img = image_subtract(pruned_img, endpoints)
-
-    # Make debugging image
-    pruned_plot = np.zeros(skel_img.shape[:2], np.uint8)
-    pruned_plot = cv2.cvtColor(pruned_plot, cv2.COLOR_GRAY2RGB)
-    skel_obj, skel_hierarchy = _cv2_findcontours(bin_img=pruned_img)
-    pruned_obj, pruned_hierarchy = _cv2_findcontours(bin_img=pruned_img)
-
-    # Reset debug mode
-    params.debug = debug
-
-    cv2.drawContours(pruned_plot, skel_obj, -1, (0, 0, 255), params.line_thickness,
-                     lineType=8, hierarchy=skel_hierarchy)
-    cv2.drawContours(pruned_plot, pruned_obj, -1, (255, 255, 255), params.line_thickness,
-                     lineType=8, hierarchy=pruned_hierarchy)
-
-    return pruned_img
diff --git a/plantcv/plantcv/morphology/find_tips.py b/plantcv/plantcv/morphology/find_tips.py
index efd396ddd..ad602dda2 100644
--- a/plantcv/plantcv/morphology/find_tips.py
+++ b/plantcv/plantcv/morphology/find_tips.py
@@ -1,84 +1,9 @@
 """Find tips from skeleton image."""
 import os
-import cv2
-import numpy as np
 from plantcv.plantcv import params
-from plantcv.plantcv import dilate
 from plantcv.plantcv import outputs
 from plantcv.plantcv._debug import _debug
-from plantcv.plantcv._helpers import _cv2_findcontours
-
-
-def _find_tips(skel_img, mask=None):
-    """Helper function to find tips in skeletonized image.
-    The endpoints algorithm was inspired by Jean-Patrick Pommier: https://gist.github.com/jeanpat/5712699
-
-    Inputs:
-    skel_img    = Skeletonized image
-    mask        = (Optional) binary mask for debugging. If provided, debug image will be overlaid on the mask.
-    label       = Optional label parameter, modifies the variable name of
-                  observations recorded (default = pcv.params.sample_label).
-    Returns:
-    tip_img   = Image with just tips, rest 0
-
-    :param skel_img: numpy.ndarray
-    :param mask: numpy.ndarray
-    :param label: str
-    :return tip_img: numpy.ndarray
-    """
-    # In a kernel: 1 values line up with 255s, -1s line up with 0s, and 0s correspond to dont care
-    endpoint1 = np.array([[-1, -1, -1],
-                          [-1, 1, -1],
-                          [0, 1,  0]])
-    endpoint2 = np.array([[-1, -1, -1],
-                          [-1, 1, 0],
-                          [-1, 0, 1]])
-
-    endpoint3 = np.rot90(endpoint1)
-    endpoint4 = np.rot90(endpoint2)
-    endpoint5 = np.rot90(endpoint3)
-    endpoint6 = np.rot90(endpoint4)
-    endpoint7 = np.rot90(endpoint5)
-    endpoint8 = np.rot90(endpoint6)
-
-    endpoints = [endpoint1, endpoint2, endpoint3, endpoint4, endpoint5, endpoint6, endpoint7, endpoint8]
-    tip_img = np.zeros(skel_img.shape[:2], dtype=int)
-    for endpoint in endpoints:
-        tip_img = np.logical_or(cv2.morphologyEx(skel_img, op=cv2.MORPH_HITMISS, kernel=endpoint,
-                                                 borderType=cv2.BORDER_CONSTANT, borderValue=0), tip_img)
-    tip_img = tip_img.astype(np.uint8) * 255
-    # Store debug
-    debug = params.debug
-    params.debug = None
-    tip_objects, _ = _cv2_findcontours(bin_img=tip_img)
-
-    if mask is None:
-        # Make debugging image
-        dilated_skel = dilate(skel_img, params.line_thickness, 1)
-        tip_plot = cv2.cvtColor(dilated_skel, cv2.COLOR_GRAY2RGB)
-
-    else:
-        # Make debugging image on mask
-        mask_copy = mask.copy()
-        tip_plot = cv2.cvtColor(mask_copy, cv2.COLOR_GRAY2RGB)
-        skel_obj, skel_hier = _cv2_findcontours(bin_img=skel_img)
-        cv2.drawContours(tip_plot, skel_obj, -1, (150, 150, 150), params.line_thickness,
-                         lineType=8, hierarchy=skel_hier)
-
-    # Initialize list of tip data points
-    tip_list = []
-    tip_labels = []
-    for i, tip in enumerate(tip_objects):
-        x, y = tip.ravel()[:2]
-        coord = (int(x), int(y))
-        tip_list.append(coord)
-        tip_labels.append(i)
-        cv2.circle(tip_plot, (x, y), params.line_thickness, (0, 255, 0), -1)
-
-    # Reset debug mode
-    params.debug = debug
-
-    return tip_img, tip_list, tip_labels
+from plantcv.plantcv._helpers import _find_tips
 
 
 def find_tips(skel_img, mask=None, label=None):
diff --git a/plantcv/plantcv/morphology/prune.py b/plantcv/plantcv/morphology/prune.py
index e71b16dfa..4edbf9ac0 100644
--- a/plantcv/plantcv/morphology/prune.py
+++ b/plantcv/plantcv/morphology/prune.py
@@ -5,11 +5,9 @@
 import numpy as np
 from plantcv.plantcv import params
 from plantcv.plantcv import image_subtract
-from plantcv.plantcv.morphology import segment_sort
-from plantcv.plantcv.morphology import segment_skeleton
-from plantcv.plantcv.morphology import _iterative_prune
+from plantcv.plantcv.morphology import segment_sort, segment_skeleton
 from plantcv.plantcv._debug import _debug
-from plantcv.plantcv._helpers import _cv2_findcontours
+from plantcv.plantcv._helpers import _cv2_findcontours, _iterative_prune
 
 
 def prune(skel_img, size=0, mask=None):
diff --git a/plantcv/plantcv/morphology/segment_curvature.py b/plantcv/plantcv/morphology/segment_curvature.py
index c44cacba6..94ee8c85b 100644
--- a/plantcv/plantcv/morphology/segment_curvature.py
+++ b/plantcv/plantcv/morphology/segment_curvature.py
@@ -5,11 +5,10 @@
 from plantcv.plantcv import params
 from plantcv.plantcv import outputs
 from plantcv.plantcv import color_palette
-from plantcv.plantcv.morphology import _find_tips
 from plantcv.plantcv.morphology import segment_path_length
 from plantcv.plantcv.morphology import segment_euclidean_length
 from plantcv.plantcv._debug import _debug
-from plantcv.plantcv._helpers import _cv2_findcontours
+from plantcv.plantcv._helpers import _cv2_findcontours, _find_tips
 
 
 def segment_curvature(segmented_img, objects, label=None):
diff --git a/plantcv/plantcv/morphology/segment_ends.py b/plantcv/plantcv/morphology/segment_ends.py
index 0d9bcf27a..5a1ccc54b 100644
--- a/plantcv/plantcv/morphology/segment_ends.py
+++ b/plantcv/plantcv/morphology/segment_ends.py
@@ -5,9 +5,7 @@
 from plantcv.plantcv import dilate, logical_and
 from plantcv.plantcv import params, outputs
 from plantcv.plantcv._debug import _debug
-from plantcv.plantcv.morphology import _iterative_prune, _find_tips
-from plantcv.plantcv._helpers import _cv2_findcontours
-
+from plantcv.plantcv._helpers import _cv2_findcontours, _find_tips, _iterative_prune
 
 def segment_ends(skel_img, leaf_objects, mask=None, label=None):
     """Find tips and segment branch points .
diff --git a/plantcv/plantcv/morphology/segment_euclidean_length.py b/plantcv/plantcv/morphology/segment_euclidean_length.py
index 269106d39..e2422ff44 100644
--- a/plantcv/plantcv/morphology/segment_euclidean_length.py
+++ b/plantcv/plantcv/morphology/segment_euclidean_length.py
@@ -7,8 +7,7 @@
 from plantcv.plantcv import fatal_error
 from plantcv.plantcv import color_palette
 from plantcv.plantcv._debug import _debug
-from plantcv.plantcv._helpers import _cv2_findcontours
-from plantcv.plantcv.morphology import _find_tips
+from plantcv.plantcv._helpers import _cv2_findcontours, _find_tips
 from scipy.spatial.distance import euclidean
 
 
diff --git a/plantcv/plantcv/morphology/segment_insertion_angle.py b/plantcv/plantcv/morphology/segment_insertion_angle.py
index 9c84ce570..9e18f589a 100644
--- a/plantcv/plantcv/morphology/segment_insertion_angle.py
+++ b/plantcv/plantcv/morphology/segment_insertion_angle.py
@@ -9,11 +9,9 @@
 from plantcv.plantcv import logical_and
 from plantcv.plantcv import fatal_error
 from plantcv.plantcv import color_palette
-from plantcv.plantcv.morphology import _iterative_prune
-from plantcv.plantcv.morphology import _find_tips
 from plantcv.plantcv.morphology.segment_tangent_angle import _slope_to_intesect_angle
 from plantcv.plantcv._debug import _debug
-from plantcv.plantcv._helpers import _cv2_findcontours
+from plantcv.plantcv._helpers import _cv2_findcontours, _find_tips, _iterative_prune
 
 
 def segment_insertion_angle(skel_img, segmented_img, leaf_objects, stem_objects, size, label=None):
diff --git a/plantcv/plantcv/morphology/segment_sort.py b/plantcv/plantcv/morphology/segment_sort.py
index 152f99884..e797871b9 100644
--- a/plantcv/plantcv/morphology/segment_sort.py
+++ b/plantcv/plantcv/morphology/segment_sort.py
@@ -6,7 +6,7 @@
 from plantcv.plantcv import dilate
 from plantcv.plantcv import params
 from plantcv.plantcv import logical_and
-from plantcv.plantcv.morphology import _find_tips
+from plantcv.plantcv._helpers import _find_tips
 from plantcv.plantcv._debug import _debug
 
 
diff --git a/plantcv/plantcv/morphology/segment_tangent_angle.py b/plantcv/plantcv/morphology/segment_tangent_angle.py
index 6a5d86938..a281a929d 100644
--- a/plantcv/plantcv/morphology/segment_tangent_angle.py
+++ b/plantcv/plantcv/morphology/segment_tangent_angle.py
@@ -6,9 +6,8 @@
 from plantcv.plantcv import params
 from plantcv.plantcv import outputs
 from plantcv.plantcv import color_palette
-from plantcv.plantcv.morphology import _iterative_prune
 from plantcv.plantcv._debug import _debug
-from plantcv.plantcv._helpers import _cv2_findcontours
+from plantcv.plantcv._helpers import _cv2_findcontours, _iterative_prune
 
 
 def _slope_to_intesect_angle(m1, m2):
diff --git a/tests/plantcv/morphology/test_prune.py b/tests/plantcv/morphology/test_prune.py
index ab09fdc65..cc2317e76 100644
--- a/tests/plantcv/morphology/test_prune.py
+++ b/tests/plantcv/morphology/test_prune.py
@@ -1,6 +1,6 @@
 import cv2
 import numpy as np
-from plantcv.plantcv.morphology import prune, _iterative_prune
+from plantcv.plantcv.morphology import prune
 
 
 def test_prune(morphology_test_data):
@@ -22,10 +22,3 @@ def test_prune_size0(morphology_test_data):
     skeleton = cv2.imread(morphology_test_data.skel_img, -1)
     pruned_img, _, _ = prune(skel_img=skeleton, size=0)
     assert np.sum(pruned_img) == np.sum(skeleton)
-
-
-def test_iterative_prune(morphology_test_data):
-    """Test for PlantCV."""
-    skeleton = cv2.imread(morphology_test_data.skel_img, -1)
-    pruned_img = _iterative_prune(skel_img=skeleton, size=3)
-    assert np.sum(pruned_img) < np.sum(skeleton)

From 554b49925ce8c67d24d9bcdf886f5013c6f0b57f Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Mon, 23 Dec 2024 16:46:33 -0600
Subject: [PATCH 25/36] whitespace fixes

---
 plantcv/plantcv/morphology/find_tips.py    | 2 +-
 plantcv/plantcv/morphology/segment_ends.py | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/plantcv/plantcv/morphology/find_tips.py b/plantcv/plantcv/morphology/find_tips.py
index ad602dda2..4831c8772 100644
--- a/plantcv/plantcv/morphology/find_tips.py
+++ b/plantcv/plantcv/morphology/find_tips.py
@@ -26,7 +26,7 @@ def find_tips(skel_img, mask=None, label=None):
     tip_img, tip_list, tip_labels = _find_tips(skel_img=skel_img, mask=mask)
 
     _debug(visual=tip_img, filename=os.path.join(params.debug_outdir, f"{params.device}_skeleton_tips.png"))
-    
+
     # Set lable to params.sample_label if None
     if label is None:
         label = params.sample_label
diff --git a/plantcv/plantcv/morphology/segment_ends.py b/plantcv/plantcv/morphology/segment_ends.py
index 5a1ccc54b..3e829dfbe 100644
--- a/plantcv/plantcv/morphology/segment_ends.py
+++ b/plantcv/plantcv/morphology/segment_ends.py
@@ -7,6 +7,7 @@
 from plantcv.plantcv._debug import _debug
 from plantcv.plantcv._helpers import _cv2_findcontours, _find_tips, _iterative_prune
 
+
 def segment_ends(skel_img, leaf_objects, mask=None, label=None):
     """Find tips and segment branch points .
 

From f802504b914af0b4925bf6180c98fd3c71a89ed2 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Thu, 2 Jan 2025 09:26:22 -0600
Subject: [PATCH 26/36] move segment_end sorting logic into _helpers

---
 plantcv/plantcv/_helpers.py                | 50 ++++++++++++++++++++++
 plantcv/plantcv/morphology/segment_ends.py | 41 ++----------------
 2 files changed, 53 insertions(+), 38 deletions(-)

diff --git a/plantcv/plantcv/_helpers.py b/plantcv/plantcv/_helpers.py
index 47a60bb01..a4192af17 100644
--- a/plantcv/plantcv/_helpers.py
+++ b/plantcv/plantcv/_helpers.py
@@ -8,6 +8,56 @@
 import pandas as pd
 
 
+def _find_segment_ends(skel_img, leaf_objects, plotting_img, size):
+    """Find both segment ends and sort into tips or inner branchpoints.
+
+    Inputs:
+    skel_img         = Skeletonized image
+    leaf_objects     = List of leaf segments
+    plotting_img     = Mask for debugging, might be a copy of the Skeletonized image
+    size             = Size of inner segment ends (in pixels)
+
+    :param skel_img: numpy.ndarray
+    :param leaf_objects: list
+    :param plotting_img: numpy.ndarray
+    """
+    labeled_img = cv2.cvtColor(plotting_img, cv2.COLOR_GRAY2RGB)
+    tips, _, _ = _find_tips(skel_img)
+    # Initialize list of tip data points
+    labels = []
+    tip_list = []
+    inner_list = []
+
+    # Find segment end coordinates
+    for i in range(len(leaf_objects)):
+        labels.append(i)
+        # Draw leaf objects
+        find_segment_tangents = np.zeros(labeled_img.shape[:2], np.uint8)
+        cv2.drawContours(find_segment_tangents, leaf_objects, i, 255, 1, lineType=8)
+        cv2.drawContours(labeled_img, leaf_objects, i, (150, 150, 150), params.line_thickness, lineType=8)  # segments debug
+        # Prune back ends of leaves
+        pruned_segment = _iterative_prune(find_segment_tangents, size)
+        # Segment ends are the portions pruned off
+        ends = find_segment_tangents - pruned_segment
+        segment_end_obj, _ = _cv2_findcontours(bin_img=ends)
+        # Determine if a segment is segment tip or branch point
+        for j, obj in enumerate(segment_end_obj):
+            segment_plot = np.zeros(skel_img.shape[:2], np.uint8)
+            cv2.drawContours(segment_plot, obj, -1, 255, 1, lineType=8)
+            segment_plot = dilate(segment_plot, 3, 1)
+            overlap_img = logical_and(segment_plot, tips)
+            x, y = segment_end_obj[j].ravel()[:2]
+            coord = (int(x), int(y))
+            # If none of the tips are within a segment_end then it's an insertion segment
+            if np.sum(overlap_img) == 0:
+                inner_list.append(coord)
+                cv2.circle(labeled_img, coord, params.line_thickness, (50, 0, 255), -1)  # Red auricles
+            else:
+                tip_list.append(coord)
+                cv2.circle(labeled_img, coord, params.line_thickness, (0, 255, 0), -1)  # green tips
+                
+    return labeled_img, tip_list, inner_list, labels
+
 def _iterative_prune(skel_img, size):
     """Iteratively remove endpoints (tips) from a skeletonized image.
     The pruning algorithm was inspired by Jean-Patrick Pommier: https://gist.github.com/jeanpat/5712699
diff --git a/plantcv/plantcv/morphology/segment_ends.py b/plantcv/plantcv/morphology/segment_ends.py
index 3e829dfbe..99e08a216 100644
--- a/plantcv/plantcv/morphology/segment_ends.py
+++ b/plantcv/plantcv/morphology/segment_ends.py
@@ -1,11 +1,8 @@
 # Find both segment end coordinates
 import os
-import cv2
-import numpy as np
-from plantcv.plantcv import dilate, logical_and
 from plantcv.plantcv import params, outputs
 from plantcv.plantcv._debug import _debug
-from plantcv.plantcv._helpers import _cv2_findcontours, _find_tips, _iterative_prune
+from plantcv.plantcv._helpers import _find_segment_ends
 
 
 def segment_ends(skel_img, leaf_objects, mask=None, label=None):
@@ -30,40 +27,8 @@ def segment_ends(skel_img, leaf_objects, mask=None, label=None):
         labeled_img = skel_img.copy()
     else:
         labeled_img = mask.copy()
-    labeled_img = cv2.cvtColor(labeled_img, cv2.COLOR_GRAY2RGB)
-    tips, _, _ = _find_tips(skel_img)
-    # Initialize list of tip data points
-    tip_list = []
-    labels = []
-    inner_list = []
-
-    # Find segment end coordinates
-    for i in range(len(leaf_objects)):
-        labels.append(i)
-        # Draw leaf objects
-        find_segment_tangents = np.zeros(labeled_img.shape[:2], np.uint8)
-        cv2.drawContours(find_segment_tangents, leaf_objects, i, 255, 1, lineType=8)
-        cv2.drawContours(labeled_img, leaf_objects, i, (150, 150, 150), params.line_thickness, lineType=8)  # segments debug
-        # Prune back ends of leaves
-        pruned_segment = _iterative_prune(find_segment_tangents, 1)
-        # Segment ends are the portions pruned off
-        ends = find_segment_tangents - pruned_segment
-        segment_end_obj, _ = _cv2_findcontours(bin_img=ends)
-        # Determine if a segment is segment tip or branch point
-        for j, obj in enumerate(segment_end_obj):
-            segment_plot = np.zeros(skel_img.shape[:2], np.uint8)
-            cv2.drawContours(segment_plot, obj, -1, 255, 1, lineType=8)
-            segment_plot = dilate(segment_plot, 3, 1)
-            overlap_img = logical_and(segment_plot, tips)
-            x, y = segment_end_obj[j].ravel()[:2]
-            coord = (int(x), int(y))
-            # If none of the tips are within a segment_end then it's an insertion segment
-            if np.sum(overlap_img) == 0:
-                inner_list.append(coord)
-                cv2.circle(labeled_img, coord, params.line_thickness, (50, 0, 255), -1)  # Red auricles
-            else:
-                tip_list.append(coord)
-                cv2.circle(labeled_img, coord, params.line_thickness, (0, 255, 0), -1)  # green tips
+    labeled_img, tip_list, inner_list, labels = _find_segment_ends(
+        skel_img=skel_img, leaf_objects=leaf_objects, plotting_img=labeled_img, size=1)
     # Set lable to params.sample_label if None
     if label is None:
         label = params.sample_label

From d8fd5c017d8cc3812cb6fe5055b8a00ef1515a7b Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Thu, 2 Jan 2025 09:36:37 -0600
Subject: [PATCH 27/36] add logic for returning the optimal segment assignment

---
 plantcv/plantcv/morphology/segment_ends.py | 20 +++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

diff --git a/plantcv/plantcv/morphology/segment_ends.py b/plantcv/plantcv/morphology/segment_ends.py
index 99e08a216..bfe31a0c0 100644
--- a/plantcv/plantcv/morphology/segment_ends.py
+++ b/plantcv/plantcv/morphology/segment_ends.py
@@ -1,5 +1,6 @@
 # Find both segment end coordinates
 import os
+import numpy as np
 from plantcv.plantcv import params, outputs
 from plantcv.plantcv._debug import _debug
 from plantcv.plantcv._helpers import _find_segment_ends
@@ -14,10 +15,15 @@ def segment_ends(skel_img, leaf_objects, mask=None, label=None):
     mask             = (Optional) binary mask for debugging. If provided, debug image will be overlaid on the mask.
     label            = Optional label parameter, modifies the variable name of
                        observations recorded (default = pcv.params.sample_label).
+                       
+    Returns:
+    sorted_ids       = Optimal assignment of leaf objects based on inner-segment y-coordinates
 
     :param segmented_img: numpy.ndarray
-    :param objects: list
+    :param leaf_objects: list
+    :param mask: numpy.ndarray
     :param label: str
+    :return sorted_ids: list
     """
     # Store debug
     debug = params.debug
@@ -27,6 +33,7 @@ def segment_ends(skel_img, leaf_objects, mask=None, label=None):
         labeled_img = skel_img.copy()
     else:
         labeled_img = mask.copy()
+    # Find and sort segment ends, and create debug image
     labeled_img, tip_list, inner_list, labels = _find_segment_ends(
         skel_img=skel_img, leaf_objects=leaf_objects, plotting_img=labeled_img, size=1)
     # Set lable to params.sample_label if None
@@ -44,3 +51,14 @@ def segment_ends(skel_img, leaf_objects, mask=None, label=None):
     # Reset debug mode
     params.debug = debug
     _debug(visual=labeled_img, filename=os.path.join(params.debug_outdir, f"{params.device}_segment_ends.png"))
+    
+    # Determine optimal segment order by y-coordinate order
+    d = {} 
+    for i, coord in enumerate(inner_list):
+        d[coord[1]] = i 
+
+    keys = list(d.keys())
+    values = list(d.values())
+    sorted_key_index = np.argsort(keys)
+    sorted_ids = [values[i] for i in sorted_key_index]
+    return sorted_ids[::-1]

From 0b296b15bd0a53dee2f1f1ba6ac09f05fcf124e9 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Thu, 2 Jan 2025 09:44:47 -0600
Subject: [PATCH 28/36] updating.md add segment_ends

---
 docs/updating.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/docs/updating.md b/docs/updating.md
index 25566975f..25e0ee404 100644
--- a/docs/updating.md
+++ b/docs/updating.md
@@ -685,6 +685,11 @@ pages for more details on the input and output variable types.
 * post v3.11: labeled_img = **plantcv.morphology.segment_curvature**(*segmented_img, objects, label="default"*)
 * post v4.0: labeled_img = **plantcv.morphology.segment_curvature**(*segmented_img, objects, label=None*)
 
+#### plantcv.morphology.segment_ends 
+
+* pre v4.6: NA
+* post v4.6: **plantcv.morphology.segment_ends**(*skel_img, leaf_objects, mask=None, label=None*)
+
 #### plantcv.morphology.segment_euclidean_length
 
 * pre v3.3: NA

From 6fde9cd0e0657eac3ffa746a61ea4ee9b2e3cf78 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Thu, 2 Jan 2025 10:35:18 -0600
Subject: [PATCH 29/36] Create segment_ends.md

---
 docs/segment_ends.md | 60 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 docs/segment_ends.md

diff --git a/docs/segment_ends.md b/docs/segment_ends.md
new file mode 100644
index 000000000..9e9e454d6
--- /dev/null
+++ b/docs/segment_ends.md
@@ -0,0 +1,60 @@
+## Identify Segment Ends
+
+Find segment tip and inner branch-point coordinates, and sort them by the y-coordinates of the branch points
+
+**plantcv.morphology.segment_ends**(*skel_img, leaf_objects, mask=None, label=None*)
+
+**returns** Optimal assignment of segment IDs
+
+- **Parameters:**
+    - skel_img - Skeleton image (output from [plantcv.morphology.skeletonize](skeletonize.md))
+    - leaf_objects - Secondary segment objects (output from [plantcv.morphology.segment_sort](segment_sort.md)).
+    - mask - Binary mask for plotting. If provided, segmented and labeled image will be overlaid on the mask (optional).
+    - label - Optional label parameter, modifies the variable name of observations recorded. (default = `pcv.params.sample_label`)
+- **Context:**
+    - Aims to sort leaf objects by biological age. This tends to work somewhat consistently for grass species that have leav
+
+**Reference Images**
+
+![Screenshot](img/documentation_images/segment_id/skeleton_image.jpg)
+
+![Screenshot](img/documentation_images/segment_id/mask_image.jpg)
+
+```python
+
+from plantcv import plantcv as pcv
+
+# Set global debug behavior to None (default), "print" (to file), 
+# or "plot" (Jupyter Notebooks or X11)
+pcv.params.debug = "plot"
+
+# Adjust line thickness with the global line thickness parameter (default = 5)
+pcv.params.line_thickness = 3 
+
+sorted_ids = pcv.morphology.segment_ends(skel_img=skeleton,
+                                         leaf_objects=leaf_obj,
+                                         mask=plant_mask,
+                                         label="leaves")
+
+segmented_img, leaves_labeled = pcv.morphology.segment_id(skel_img=skeleton, 
+                                                          objects=leaf_obj,
+                                                          mask=plant_mask,
+                                                          optimal_assignment=sorted_ids)
+# Without optimal assignment leaf tips are used by default
+segmented_img, leaves_labeled = pcv.morphology.segment_id(skel_img=skeleton, 
+                                                          objects=leaf_obj,
+                                                          mask=plant_mask)
+
+```
+
+*Input Segmented Image, Leaves Only with Mask*
+
+![Screenshot](img/documentation_images//.jpg)
+
+
+
+*Labeled Image, Leaves Only with Mask without Optimal Reassignment of segments*
+
+![Screenshot](img/documentation_images/segment_id/labeled_leaves_mask.jpg)
+
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/main/plantcv/plantcv/morphology/segment_ends.py)

From a8c74a5642a778bd1a645be1b166db038707b77f Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Thu, 2 Jan 2025 15:07:58 -0600
Subject: [PATCH 30/36] whitespace deepsource fixes

---
 plantcv/plantcv/_helpers.py                | 3 ++-
 plantcv/plantcv/morphology/segment_ends.py | 9 ++++-----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/plantcv/plantcv/_helpers.py b/plantcv/plantcv/_helpers.py
index a4192af17..0899edc23 100644
--- a/plantcv/plantcv/_helpers.py
+++ b/plantcv/plantcv/_helpers.py
@@ -55,9 +55,10 @@ def _find_segment_ends(skel_img, leaf_objects, plotting_img, size):
             else:
                 tip_list.append(coord)
                 cv2.circle(labeled_img, coord, params.line_thickness, (0, 255, 0), -1)  # green tips
-                
+
     return labeled_img, tip_list, inner_list, labels
 
+
 def _iterative_prune(skel_img, size):
     """Iteratively remove endpoints (tips) from a skeletonized image.
     The pruning algorithm was inspired by Jean-Patrick Pommier: https://gist.github.com/jeanpat/5712699
diff --git a/plantcv/plantcv/morphology/segment_ends.py b/plantcv/plantcv/morphology/segment_ends.py
index bfe31a0c0..6aff72ec4 100644
--- a/plantcv/plantcv/morphology/segment_ends.py
+++ b/plantcv/plantcv/morphology/segment_ends.py
@@ -15,7 +15,7 @@ def segment_ends(skel_img, leaf_objects, mask=None, label=None):
     mask             = (Optional) binary mask for debugging. If provided, debug image will be overlaid on the mask.
     label            = Optional label parameter, modifies the variable name of
                        observations recorded (default = pcv.params.sample_label).
-                       
+
     Returns:
     sorted_ids       = Optimal assignment of leaf objects based on inner-segment y-coordinates
 
@@ -51,12 +51,11 @@ def segment_ends(skel_img, leaf_objects, mask=None, label=None):
     # Reset debug mode
     params.debug = debug
     _debug(visual=labeled_img, filename=os.path.join(params.debug_outdir, f"{params.device}_segment_ends.png"))
-    
+
     # Determine optimal segment order by y-coordinate order
-    d = {} 
+    d = {}
     for i, coord in enumerate(inner_list):
-        d[coord[1]] = i 
-
+        d[coord[1]] = i
     keys = list(d.keys())
     values = list(d.values())
     sorted_key_index = np.argsort(keys)

From 85c2c9fe20a6a1bcc6d4929b7728aa5bd26aad88 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Fri, 3 Jan 2025 09:03:24 -0600
Subject: [PATCH 31/36] add debug images for segment ends

---
 .../segment_ends/segment_end_pts.png            | Bin 0 -> 27889 bytes
 .../segment_ends/setaria_mask.png               | Bin 0 -> 23563 bytes
 docs/segment_ends.md                            |  14 +++-----------
 3 files changed, 3 insertions(+), 11 deletions(-)
 create mode 100644 docs/img/documentation_images/segment_ends/segment_end_pts.png
 create mode 100644 docs/img/documentation_images/segment_ends/setaria_mask.png

diff --git a/docs/img/documentation_images/segment_ends/segment_end_pts.png b/docs/img/documentation_images/segment_ends/segment_end_pts.png
new file mode 100644
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diff --git a/docs/segment_ends.md b/docs/segment_ends.md
index 9e9e454d6..d087398e4 100644
--- a/docs/segment_ends.md
+++ b/docs/segment_ends.md
@@ -16,9 +16,7 @@ Find segment tip and inner branch-point coordinates, and sort them by the y-coor
 
 **Reference Images**
 
-![Screenshot](img/documentation_images/segment_id/skeleton_image.jpg)
-
-![Screenshot](img/documentation_images/segment_id/mask_image.jpg)
+![Screenshot](img/documentation_images/segment_ends/setaria_mask.png)
 
 ```python
 
@@ -47,14 +45,8 @@ segmented_img, leaves_labeled = pcv.morphology.segment_id(skel_img=skeleton,
 
 ```
 
-*Input Segmented Image, Leaves Only with Mask*
-
-![Screenshot](img/documentation_images//.jpg)
-
-
-
-*Labeled Image, Leaves Only with Mask without Optimal Reassignment of segments*
+*Segment end points Debug*
 
-![Screenshot](img/documentation_images/segment_id/labeled_leaves_mask.jpg)
+![Screenshot](img/documentation_images/segment_ends/segment_end_pts.png)
 
 **Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/main/plantcv/plantcv/morphology/segment_ends.py)

From 869c23259bfdda0272824bd7ff0b3f5007aef7a7 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Fri, 3 Jan 2025 14:33:04 -0600
Subject: [PATCH 32/36] return sorted objs instead of ordered labels

---
 plantcv/plantcv/morphology/segment_ends.py | 11 ++++++-----
 plantcv/plantcv/morphology/segment_id.py   | 10 +++++-----
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/plantcv/plantcv/morphology/segment_ends.py b/plantcv/plantcv/morphology/segment_ends.py
index 6aff72ec4..fed10e0fa 100644
--- a/plantcv/plantcv/morphology/segment_ends.py
+++ b/plantcv/plantcv/morphology/segment_ends.py
@@ -7,7 +7,7 @@
 
 
 def segment_ends(skel_img, leaf_objects, mask=None, label=None):
-    """Find tips and segment branch points .
+    """Find tips and segment branch points.
 
     Inputs:
     skel_img         = Skeletonized image
@@ -17,7 +17,7 @@ def segment_ends(skel_img, leaf_objects, mask=None, label=None):
                        observations recorded (default = pcv.params.sample_label).
 
     Returns:
-    sorted_ids       = Optimal assignment of leaf objects based on inner-segment y-coordinates
+    sorted_obs       = Reordered segments based on segment branch point y-coordinates
 
     :param segmented_img: numpy.ndarray
     :param leaf_objects: list
@@ -55,9 +55,10 @@ def segment_ends(skel_img, leaf_objects, mask=None, label=None):
     # Determine optimal segment order by y-coordinate order
     d = {}
     for i, coord in enumerate(inner_list):
-        d[coord[1]] = i
+        d[coord[1]] = leaf_objects[i]  # y-coord is the key and index the value
     keys = list(d.keys())
     values = list(d.values())
     sorted_key_index = np.argsort(keys)
-    sorted_ids = [values[i] for i in sorted_key_index]
-    return sorted_ids[::-1]
+    sorted_objs = [values[i] for i in sorted_key_index[::-1]]
+
+    return sorted_objs
diff --git a/plantcv/plantcv/morphology/segment_id.py b/plantcv/plantcv/morphology/segment_id.py
index a1a89e109..d7c159959 100644
--- a/plantcv/plantcv/morphology/segment_id.py
+++ b/plantcv/plantcv/morphology/segment_id.py
@@ -45,10 +45,10 @@ def segment_id(skel_img, objects, mask=None, optimal_assignment=None):
             color_index = optimal_assignment[i]
         else:
             color_index = i
-        cv2.drawContours(segmented_img, cnt, -1, rand_color[color_index], params.line_thickness, lineType=8)
+        cv2.drawContours(segmented_img, cnt, -1, rand_color[i], params.line_thickness, lineType=8)
         # Store coordinates for labels
-        label_coord_x.append(objects[i][0][0][0])
-        label_coord_y.append(objects[i][0][0][1])
+        label_coord_x.append(objects[color_index][0][0][0])
+        label_coord_y.append(objects[color_index][0][0][1])
 
     labeled_img = segmented_img.copy()
 
@@ -61,8 +61,8 @@ def segment_id(skel_img, objects, mask=None, optimal_assignment=None):
             text = f"{i}"
             color_index = i
         # Label segments
-        w = label_coord_x[i]
-        h = label_coord_y[i]
+        w = label_coord_x[color_index]
+        h = label_coord_y[color_index]
         cv2.putText(img=labeled_img, text=text, org=(w, h), fontFace=cv2.FONT_HERSHEY_SIMPLEX,
                     fontScale=params.text_size, color=rand_color[color_index], thickness=params.text_thickness)
 

From 2e4149dd33b2adf0220bfc7357567accea8f8bc3 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Fri, 3 Jan 2025 14:57:29 -0600
Subject: [PATCH 33/36] Update mkdocs.yml

---
 mkdocs.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/mkdocs.yml b/mkdocs.yml
index a0e83e2d7..d625c7455 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -118,6 +118,7 @@ nav:
         - 'Segment Angles': segment_angle.md
         - 'Combine Segments': segment_combine.md
         - 'Segment Curvature': segment_curvature.md
+        - 'Segment Ends': segment_ends.md
         - 'Segment Euclidean Length': segment_euclidean_length.md
         - 'Segment ID': segment_id.md
         - 'Segment Insertion Angle': segment_insertion_angle.md

From fa7f689548616f834b87d829b53b9d70634d7c8e Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Fri, 3 Jan 2025 14:57:43 -0600
Subject: [PATCH 34/36] update docs to reflect new sorting approach

---
 docs/segment_ends.md | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/docs/segment_ends.md b/docs/segment_ends.md
index d087398e4..b51b3db12 100644
--- a/docs/segment_ends.md
+++ b/docs/segment_ends.md
@@ -4,7 +4,7 @@ Find segment tip and inner branch-point coordinates, and sort them by the y-coor
 
 **plantcv.morphology.segment_ends**(*skel_img, leaf_objects, mask=None, label=None*)
 
-**returns** Optimal assignment of segment IDs
+**returns** Re-ordered leaf segments
 
 - **Parameters:**
     - skel_img - Skeleton image (output from [plantcv.morphology.skeletonize](skeletonize.md))
@@ -29,18 +29,17 @@ pcv.params.debug = "plot"
 # Adjust line thickness with the global line thickness parameter (default = 5)
 pcv.params.line_thickness = 3 
 
-sorted_ids = pcv.morphology.segment_ends(skel_img=skeleton,
+sorted_obs = pcv.morphology.segment_ends(skel_img=skeleton,
                                          leaf_objects=leaf_obj,
                                          mask=plant_mask,
                                          label="leaves")
 
 segmented_img, leaves_labeled = pcv.morphology.segment_id(skel_img=skeleton, 
                                                           objects=leaf_obj,
-                                                          mask=plant_mask,
-                                                          optimal_assignment=sorted_ids)
+                                                          mask=plant_mask
 # Without optimal assignment leaf tips are used by default
 segmented_img, leaves_labeled = pcv.morphology.segment_id(skel_img=skeleton, 
-                                                          objects=leaf_obj,
+                                                          objects=sorted_obs,
                                                           mask=plant_mask)
 
 ```

From 2b8480ad23408935205c9b8ae893791856593c1c Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Wed, 22 Jan 2025 15:04:20 -0600
Subject: [PATCH 35/36] update segment_ends sorting logic

---
 plantcv/plantcv/morphology/segment_ends.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/plantcv/plantcv/morphology/segment_ends.py b/plantcv/plantcv/morphology/segment_ends.py
index fed10e0fa..e60790cba 100644
--- a/plantcv/plantcv/morphology/segment_ends.py
+++ b/plantcv/plantcv/morphology/segment_ends.py
@@ -55,10 +55,9 @@ def segment_ends(skel_img, leaf_objects, mask=None, label=None):
     # Determine optimal segment order by y-coordinate order
     d = {}
     for i, coord in enumerate(inner_list):
-        d[coord[1]] = leaf_objects[i]  # y-coord is the key and index the value
-    keys = list(d.keys())
+        d[i] = coord[1]  # y-coord is the key and index the value
     values = list(d.values())
-    sorted_key_index = np.argsort(keys)
-    sorted_objs = [values[i] for i in sorted_key_index[::-1]]
+    sorted_key_index = np.argsort(values)
+    sorted_objs = [leaf_objects[i] for i in sorted_key_index[::-1]]
 
     return sorted_objs

From a3d0cfffb4788e6df677127ea41f6bb9f96556a3 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Thu, 30 Jan 2025 09:34:22 -0600
Subject: [PATCH 36/36] minor tweaks to docs for clarity and accuracy

---
 docs/segment_ends.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/docs/segment_ends.md b/docs/segment_ends.md
index b51b3db12..c71a1b75e 100644
--- a/docs/segment_ends.md
+++ b/docs/segment_ends.md
@@ -9,7 +9,7 @@ Find segment tip and inner branch-point coordinates, and sort them by the y-coor
 - **Parameters:**
     - skel_img - Skeleton image (output from [plantcv.morphology.skeletonize](skeletonize.md))
     - leaf_objects - Secondary segment objects (output from [plantcv.morphology.segment_sort](segment_sort.md)).
-    - mask - Binary mask for plotting. If provided, segmented and labeled image will be overlaid on the mask (optional).
+    - mask - Binary mask for plotting. If provided, the debugging image will be overlaid on the mask (optional).
     - label - Optional label parameter, modifies the variable name of observations recorded. (default = `pcv.params.sample_label`)
 - **Context:**
     - Aims to sort leaf objects by biological age. This tends to work somewhat consistently for grass species that have leav
@@ -26,18 +26,18 @@ from plantcv import plantcv as pcv
 # or "plot" (Jupyter Notebooks or X11)
 pcv.params.debug = "plot"
 
-# Adjust line thickness with the global line thickness parameter (default = 5)
+# Adjust point thickness with the global line_thickness parameter (default = 5)
 pcv.params.line_thickness = 3 
 
 sorted_obs = pcv.morphology.segment_ends(skel_img=skeleton,
-                                         leaf_objects=leaf_obj,
+                                         leaf_objects=leaf_objs,
                                          mask=plant_mask,
                                          label="leaves")
 
 segmented_img, leaves_labeled = pcv.morphology.segment_id(skel_img=skeleton, 
-                                                          objects=leaf_obj,
+                                                          objects=leaf_objs,
                                                           mask=plant_mask
-# Without optimal assignment leaf tips are used by default
+# Without ID re-assignment
 segmented_img, leaves_labeled = pcv.morphology.segment_id(skel_img=skeleton, 
                                                           objects=sorted_obs,
                                                           mask=plant_mask)