diff --git a/Image_based/branchpointdetection.py b/Image_based/branchpointdetection.py
index ef7234b..b30df55 100644
--- a/Image_based/branchpointdetection.py
+++ b/Image_based/branchpointdetection.py
@@ -9,7 +9,7 @@
 import json
 from os.path import exists
 from bezier_cyl_2d import BezierCyl2D
-from line_seg_2d import draw_line, draw_box, draw_cross, LineSeg2D
+from line_seg_2d import LineSeg2D
 from scipy.cluster.vq import kmeans, whiten, vq
 
 class BranchPointDetection:
@@ -67,18 +67,19 @@ def __init__(self, path, image_name, b_output_debug=True, b_recalc=False):
 
         # For each of the trunk/branches, see if we have reasonable upper left/lower right points
         #   Save points in debug image
+
         if b_output_debug:
             self.images_single["marked points"] = np.copy(self.images_single["masked"])
             for im in self.images:
                 try:
                     p1 = im["stats"]["lower_left"]
                     p2 = im["stats"]["upper_right"]
-                    draw_line(im["image"], p1, p2, (128, 128, 128), 2)
-                    draw_line(self.images_single["marked points"], p1, p2, (128, 128, 128), 1)
+                    LineSeg2D.draw_line(im["image"], p1, p2, (128, 128, 128), 2)
+                    LineSeg2D.draw_line(self.images_single["marked points"], p1, p2, (128, 128, 128), 1)
 
                     pc = im["stats"]["center"]
-                    draw_cross(im["image"], pc, (128, 128, 128), 1, 2)
-                    draw_cross(self.images_single["marked points"], pc, (180, 180, 128), 1, 3)
+                    LineSeg2D.draw_cross(im["image"], pc, (128, 128, 128), 1, 2)
+                    LineSeg2D.draw_cross(self.images_single["marked points"], pc, (180, 180, 128), 1, 3)
 
                     cv2.imwrite(self.path_debug + image_name + "_" + im["name"] + "_points.png", im["image"])
                 except:
@@ -111,8 +112,8 @@ def __init__(self, path, image_name, b_output_debug=True, b_recalc=False):
                 # Draw the original, the edges, and the depth mask with the fitted quad
                 im["quad"].draw_bezier(im_orig_debug)
                 if im["quad"].is_wire():
-                    draw_cross(im_orig_debug, im["quad"].p0, (255, 0, 0), thickness=2, length=10)
-                    draw_cross(im_orig_debug, im["quad"].p2, (255, 0, 0), thickness=2, length=10)
+                    LineSeg2D.draw_cross(im_orig_debug, im["quad"].p0, (255, 0, 0), thickness=2, length=10)
+                    LineSeg2D.draw_cross(im_orig_debug, im["quad"].p2, (255, 0, 0), thickness=2, length=10)
                 else:
                     im["quad"].draw_boundary(im_orig_debug, 10)
                     im["quad"].draw_edge_rects(im_covert_back, step_size=params["step_size"], perc_width=params["width"])
@@ -158,8 +159,8 @@ def __init__(self, path, image_name, b_output_debug=True, b_recalc=False):
                 # Draw the original, the edges, and the depth mask with the fitted quad
                 im["quad_flow"].draw_bezier(im_orig_debug)
                 if im["quad_flow"].is_wire():
-                    draw_cross(im_orig_debug, im["quad_flow"].p0, (255, 0, 0), thickness=2, length=10)
-                    draw_cross(im_orig_debug, im["quad_flow"].p2, (255, 0, 0), thickness=2, length=10)
+                    LineSeg2D.draw_cross(im_orig_debug, im["quad_flow"].p0, (255, 0, 0), thickness=2, length=10)
+                    LineSeg2D.draw_cross(im_orig_debug, im["quad_flow"].p2, (255, 0, 0), thickness=2, length=10)
                 else:
                     im["quad_flow"].draw_boundary(im_orig_debug, 10)
                     im["quad_flow"].draw_edge_rects(im_covert_back, step_size=params["step_size"], perc_width=params["width"])
@@ -202,8 +203,8 @@ def __init__(self, path, image_name, b_output_debug=True, b_recalc=False):
 
         if b_output_debug:
             for p, v in self.branch_points:
-                draw_box(self.images_single["marked points"], p, (254, 128, 254), 6)
-                draw_line(self.images_single["marked points"], p, p + v, (128, 254, 254), 1)
+                LineSeg2D.draw_box(self.images_single["marked points"], p, (254, 128, 254), 6)
+                LineSeg2D.draw_line(self.images_single["marked points"], p, p + v, (128, 254, 254), 1)
 
             cv2.imwrite(self.path_debug + image_name + "_" + "_marked_joins_points.png", self.images_single["marked points"])
 
@@ -333,7 +334,7 @@ def fit_quad(self, im, b_output_debug=True):
         quad = BezierCyl2D(pts['lower_left'], pts['upper_right'], 0.5 * pts['width'])
 
         # Current parameters for the vertical leader
-        params = {"step_size": int(quad.radius_2d * 1.5), "width_mask": 1.4, "width": 0.3}
+        params = {"step_size": int(quad.radius * 1.5), "width_mask": 1.4, "width": 0.3}
 
         # Iteratively move the quad to the center of the mask
         for i in range(0, 5):
@@ -482,4 +483,4 @@ def find_branch_point(self, im_trunk, im_sidebranch):
     for im_i in range(0, 18):
         name = str(im_i)
         print(name)
-        bp = BranchPointDetection(path, name, b_output_debug=True)
+        bp = BranchPointDetection(path, name, b_output_debug=False)
diff --git a/__pycache__/bezier_cyl_3d.cpython-310.pyc b/__pycache__/bezier_cyl_3d.cpython-310.pyc
new file mode 100644
index 0000000..e125f4e
Binary files /dev/null and b/__pycache__/bezier_cyl_3d.cpython-310.pyc differ
diff --git a/bezier_cyl_3d.py b/bezier_cyl_3d.py
index 8c03cd8..a91e4a8 100644
--- a/bezier_cyl_3d.py
+++ b/bezier_cyl_3d.py
@@ -12,7 +12,9 @@
 import numpy as np
 from json import load, dump
 
-
+#switch to this
+#use sdk--> look at point cloud
+#take every 3 points and do bezier
 class BezierCyl3D:
 
     def __init__(self, p1=(0.0, 0.0, 0.0), p2=(0.5, 0.75, 0.5), p3=(1.0, 1.0, 1.0), start_radius=10.0, end_radius=20.0):
@@ -145,6 +147,7 @@ def frenet_frame(self, t):
     def _calc_radii(self):
         """ Calculate the radii along the branch
         @return a numpy array of radii"""
+        
         radii = np.linspace(self.start_radii, self.end_radii, self.n_along)
         return radii
 
@@ -152,7 +155,7 @@ def _calc_cyl_vertices(self):
         """Calculate the cylinder vertices"""
         pt = np.ones(shape=(4,))
         radii = self._calc_radii()
-
+        
         for it, t in enumerate(np.linspace(0, 1.0, self.n_along)):
             mat = self.frenet_frame(t)
             pt[0] = 0
@@ -165,6 +168,7 @@ def _calc_cyl_vertices(self):
                 pt_on_crv = mat @ pt
 
                 self.vertex_locs[it, itheta, :] = pt_on_crv[0:3].transpose()
+                
 
     def make_mesh(self):
         """ Make a 3D generalized cylinder """
@@ -237,17 +241,17 @@ def read_json(fname, bezier_crv=None, compute_mesh=True):
     from os.path import exists
     from os import mkdir
 
-    if not exists("data/DebugImages"):
-        mkdir("data/DebugImages")
+    #if not exists("data/DebugImages"):
+        #mkdir("data/DebugImages")
     branch = BezierCyl3D([506.5, 156.0, 0.0], [457.49999996771703, 478.9999900052037, 0.0], [521.5, 318.0, 0.0],
                          start_radius=10.5, end_radius=8.25)
     branch.make_mesh()
-    branch.write_mesh("data/DebugImages/check_3d_bezier1.obj")
+    branch.write_mesh("check_3d_bezier1.obj")
 
     branch = BezierCyl3D([-0.5, 0.0, 0.0], [0.0, 0.1, 0.05], [0.5, 0.0, 0.0], start_radius=0.5, end_radius=0.25)
     branch.make_mesh()
-    branch.write_mesh("data/DebugImages/check_3d_bezier2.obj")
+    branch.write_mesh("check_3d_bezier2.obj")
 
     branch.set_dims(n_along=30, n_radial=32)
     branch.make_mesh()
-    branch.write_mesh("data/DebugImages/check_3d_bezier_more_vs.obj")
+    branch.write_mesh("check_3d_bezier_more_vs.obj")
diff --git a/data/DebugImages/check_3d_bezier1.obj b/data/DebugImages/check_3d_bezier1.obj
new file mode 100644
index 0000000..f7194ef
--- /dev/null
+++ b/data/DebugImages/check_3d_bezier1.obj
@@ -0,0 +1,1793 @@
+# Branch
+v 496.119 154.425 0.0
+v 496.169 154.433 -1.02918
+v 496.318 154.455 -2.04845
+v 496.566 154.493 -3.04799
+v 496.909 154.545 -4.01818
+v 497.345 154.611 -4.94967
+v 497.868 154.691 -5.83349
+v 498.475 154.783 -6.66113
+v 499.159 154.886 -7.42462
+v 499.914 155.001 -8.11661
+v 500.733 155.125 -8.73043
+v 501.606 155.258 -9.26017
+v 502.527 155.397 -9.70074
+v 503.486 155.543 -10.0479
+v 504.475 155.693 -10.2982
+v 505.482 155.846 -10.4494
+v 506.5 156.0 -10.5
+v 507.518 156.154 -10.4494
+v 508.525 156.307 -10.2982
+v 509.514 156.457 -10.0479
+v 510.473 156.603 -9.70074
+v 511.394 156.742 -9.26017
+v 512.267 156.875 -8.73043
+v 513.086 156.999 -8.11661
+v 513.841 157.114 -7.42462
+v 514.525 157.217 -6.66113
+v 515.132 157.309 -5.83349
+v 515.655 157.389 -4.94967
+v 516.091 157.455 -4.01818
+v 516.434 157.507 -3.04799
+v 516.682 157.545 -2.04845
+v 516.831 157.567 -1.02918
+v 516.881 157.575 -1.28588e-15
+v 516.831 157.567 1.02918
+v 516.682 157.545 2.04845
+v 516.434 157.507 3.04799
+v 516.091 157.455 4.01818
+v 515.655 157.389 4.94967
+v 515.132 157.309 5.83349
+v 514.525 157.217 6.66113
+v 513.841 157.114 7.42462
+v 513.086 156.999 8.11661
+v 512.267 156.875 8.73043
+v 511.394 156.742 9.26017
+v 510.473 156.603 9.70074
+v 509.514 156.457 10.0479
+v 508.525 156.307 10.2982
+v 507.518 156.154 10.4494
+v 506.5 156.0 10.5
+v 505.482 155.846 10.4494
+v 504.475 155.693 10.2982
+v 503.486 155.543 10.0479
+v 502.527 155.397 9.70074
+v 501.606 155.258 9.26017
+v 500.733 155.125 8.73043
+v 499.914 155.001 8.11661
+v 499.159 154.886 7.42462
+v 498.475 154.783 6.66113
+v 497.868 154.691 5.83349
+v 497.345 154.611 4.94967
+v 496.909 154.545 4.01818
+v 496.566 154.493 3.04799
+v 496.318 154.455 2.04845
+v 496.169 154.433 1.02918
+v 486.849 220.427 0.0
+v 486.898 220.434 -1.00468
+v 487.044 220.454 -1.99968
+v 487.286 220.487 -2.97542
+v 487.622 220.532 -3.92251
+v 488.048 220.59 -4.83182
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+v 489.824 220.83 -7.24784
+v 490.562 220.93 -7.92336
+v 491.363 221.039 -8.52256
+v 492.218 221.154 -9.03969
+v 493.119 221.276 -9.46977
+v 494.058 221.403 -9.80864
+v 495.025 221.534 -10.053
+v 496.011 221.668 -10.2006
+v 497.006 221.802 -10.25
+v 498.002 221.937 -10.2006
+v 498.988 222.071 -10.053
+v 499.955 222.202 -9.80864
+v 500.893 222.329 -9.46977
+v 501.794 222.451 -9.03969
+v 502.649 222.566 -8.52256
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+v 505.452 222.946 -5.69459
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+v 506.726 223.118 -2.97542
+v 506.968 223.151 -1.99968
+v 507.115 223.171 -1.00468
+v 507.164 223.177 -1.25526e-15
+v 507.115 223.171 1.00468
+v 506.968 223.151 1.99968
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+v 506.39 223.073 3.92251
+v 505.964 223.015 4.83182
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+v 498.002 221.937 10.2006
+v 497.006 221.802 10.25
+v 496.011 221.668 10.2006
+v 495.025 221.534 10.053
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+v 487.286 220.487 2.97542
+v 487.044 220.454 1.99968
+v 486.898 220.434 1.00468
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+v 480.411 274.558 -0.980171
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+v 480.791 274.6 -2.90285
+v 481.12 274.636 -3.82683
+v 481.537 274.682 -4.71397
+v 482.038 274.738 -5.5557
+v 482.619 274.802 -6.34393
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+v 483.997 274.955 -7.7301
+v 484.781 275.042 -8.3147
+v 485.617 275.135 -8.81921
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+v 488.363 275.439 -9.80785
+v 489.328 275.546 -9.95185
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+v 500.242 276.756 -1.22465e-15
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+v 499.068 276.626 4.71397
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+v 495.824 276.267 8.3147
+v 494.988 276.174 8.81921
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+v 493.188 275.974 9.5694
+v 492.241 275.869 9.80785
+v 491.277 275.762 9.95185
+v 490.302 275.654 10.0
+v 489.328 275.546 9.95185
+v 488.363 275.439 9.80785
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+v 486.499 275.233 9.2388
+v 485.617 275.135 8.81921
+v 484.781 275.042 8.3147
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+v 483.274 274.875 7.07107
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+v 482.038 274.738 5.5557
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+v 480.985 317.177 -8.10683
+v 481.804 317.234 -8.59873
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+v 484.491 317.423 -9.56266
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+v 486.389 317.556 -9.75
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+v 494.967 318.157 4.59612
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+v 478.548 347.582 6.71751
+v 477.922 347.589 6.02674
+v 477.367 347.596 5.27792
+v 476.888 347.601 4.47827
+v 476.489 347.606 3.63549
+v 476.175 347.609 2.7577
+v 475.949 347.612 1.85336
+v 475.812 347.613 0.931163
+v 477.968 367.789 0.0
+v 478.011 367.778 -0.906659
+v 478.14 367.745 -1.80459
+v 478.354 367.69 -2.68513
+v 478.65 367.615 -3.53982
+v 479.027 367.519 -4.36042
+v 479.479 367.404 -5.13902
+v 480.003 367.27 -5.86814
+v 480.594 367.12 -6.54074
+v 481.245 366.954 -7.15035
+v 481.952 366.774 -7.69109
+v 482.707 366.582 -8.15777
+v 483.502 366.38 -8.54589
+v 484.33 366.169 -8.8517
+v 485.183 365.951 -9.07226
+v 486.053 365.73 -9.20546
+v 486.932 365.506 -9.25
+v 487.811 365.282 -9.20546
+v 488.681 365.061 -9.07226
+v 489.534 364.844 -8.8517
+v 490.362 364.633 -8.54589
+v 491.158 364.43 -8.15777
+v 491.912 364.238 -7.69109
+v 492.619 364.058 -7.15035
+v 493.271 363.892 -6.54074
+v 493.861 363.742 -5.86814
+v 494.385 363.608 -5.13902
+v 494.838 363.493 -4.36042
+v 495.214 363.397 -3.53982
+v 495.51 363.322 -2.68513
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diff --git a/data/DebugImages/check_3d_bezier2.obj b/data/DebugImages/check_3d_bezier2.obj
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diff --git a/marshall/Blender/generate_3d.py b/marshall/Blender/generate_3d.py
new file mode 100644
index 0000000..3e55294
--- /dev/null
+++ b/marshall/Blender/generate_3d.py
@@ -0,0 +1,76 @@
+import bpy
+import bmesh
+import os
+import numpy as np
+import camera as c
+import params as p
+from random import randint
+from mathutils import Vector, Matrix, Euler
+from math import radians
+import matplotlib.pyplot as plt
+from scipy.spatial.transform import Rotation as R
+from curve_fitting import BezierBasedDetection, Bezier
+from bpy_extras.io_utils import unpack_list
+
+
+
+class Generate_3D:   
+    def __init__(self, full_arr, x, y, z, num_pix):
+        self.full_arr = full_arr
+        self.rad = []
+        self.y = y
+        self.x = x
+        self.num_pix = num_pix
+        self.z = z
+        
+    def create_mesh(self):
+        self.set_y_x_rad()
+        
+        #bpy.data.objects.remove(bpy.data.objects['Cube'])
+
+        crv = bpy.data.curves.new('crv', 'CURVE')
+        crv.dimensions = '3D'
+        crv.fill_mode = 'FULL'
+        crv.bevel_depth = 0.045
+        crv.resolution_u = 1 
+        obj = bpy.data.objects.new('crv', crv)
+        bpy.context.scene.collection.objects.link(obj)         
+        spline = crv.splines.new(type='BEZIER')
+        
+        spline.bezier_points.add(len(self.full_arr)-1)
+        for i in range(len(self.full_arr)):
+           
+            
+            spline.bezier_points[i].co = self.full_arr[i]
+          
+            spline.bezier_points[i].radius = self.rad[i]
+               
+            print(spline.bezier_points[i].radius)
+            
+        
+        fig = plt.figure()
+        ax = fig.add_subplot(projection='3d')
+        ax.plot(*self.full_arr.T)
+        ax.axis('equal')
+        plt.show()
+        
+        blend_file_path = bpy.data.filepath
+        directory = os.path.dirname(blend_file_path)
+        target_file = os.path.join(directory, 'thisisatest.obj')
+        bpy.ops.export_scene.obj(filepath=target_file)  
+        
+    def set_y_x_rad(self):
+        camera = c.PinholeCameraModel()
+        camera.from_npz(p.cam)
+        assert isinstance(camera, c.PinholeCameraModel)
+        
+        
+        for i in range(len(self.full_arr)):
+            self.full_arr[i][0] = camera.getDeltaX(self.x[i], self.z[i])
+            self.full_arr[i][1] = camera.getDeltaY(self.y[i], self.z[i])
+            self.rad.append(camera.getDeltaX(self.num_pix[i], self.z[i]))
+            print(self.num_pix[i])
+       
+                 
+
+        
diff --git a/marshall/D435_640x480.camera.npz b/marshall/D435_640x480.camera.npz
new file mode 100644
index 0000000..9f9051c
Binary files /dev/null and b/marshall/D435_640x480.camera.npz differ
diff --git a/marshall/README.md b/marshall/README.md
new file mode 100644
index 0000000..8590555
--- /dev/null
+++ b/marshall/README.md
@@ -0,0 +1,56 @@
+# internship_summer_2023
+Work and documentation from my summer 2023 AgAID internship.
+
+# What it is
+The test_connectivity.py code takes in masks and depth images of trees, builds 3D cylinders along a bezier curve following a branch, and determines which side branches are connected to which main or "leader" branches.
+The pull depth and rgb data file takes a .mkv video and extracts depth and rgb data in whatever format you wish.--> may require changes to test_connectivity to work with different formats.
+
+# How it works
+1. Builds a Bezier curve by determining the medial axis of the white space in a mask
+   - This returns the radii, "t" value and the curve points at which the curve is evaluated, as well as a curve
+2. Finds average depth in a cross-space of the tree branch
+   - Uses numpy and opencv to do this by first drawing singular blue squares that align with the limits of the mask and the curve points, then by reading the depth image at those points
+3. Determines the closest point and distance from the end points of the side branch to the curve of the leader and picks the closest two points
+4. Determines the difference in depth between the two points
+5. Determines the angle between the two tangent lines of each points
+6. Returns a score based in those aspects that refers to how likely it is that the branches are connected (lower is better)
+7. Plots curves and points it is evaluating
+8. Uses bezier cyl 3d to generate cylinders along the curve
+9. Merges cylinder files to create a tree
+    
+# Assumptions
+- Leader and side branches are labeled as such
+- Points are ordered
+- There is a .mkv video file to work with
+- There are masks to work with
+  
+# Notes for Running
+- After cloning the repository, just run connection_test.py
+- Adjust any of the parameters to include your own depth and mask images as well as a video file (uploaded files do not currently contain the mkv file used for generation)
+- Requires OpenCV, Matplotlib, Skimage, Scipy, PyK4A, and Networkx libraries--> see Documentation for install PyK4A
+- To pull RGB and Depth data, copy the python file to the directory where the .mkv video is stored(or alter code to specify a path)
+
+# General Notes
+- The curve_fitting and camera files are contribution from [Alex You](https://github.com/osu-youa)
+- Azure camera depth data needs to be tested to confirm its conversion to meters
+- generate_3d.py works with and requires Blender to run. It uses Blender to generate a Bezier curve rather than using cylinders. Unless scaled up, it generates a small curve in meters. Radius does not currently operate as expected.
+
+# Output
+The cylinders generated produce:
+![alt text](generated_tree.png)
+As compared to:
+![alt text](leader_mask.png)
+![alt text](follower_mask.png)
+It displays in the terminal:
+![alt text](output.png)
+This shows the total score for how likely a side branch is to match to a leader branch(lower is better).
+
+# Instructions for Installing PyK4A
+- See: [Kinect on Ubuntu](https://github.com/juancarlosmiranda/azure_kinect_notes)
+- And: [PyK4A](https://github.com/etiennedub/pyk4a)
+
+# TODO:
+- Image annotations for model
+- Test camera to confirm conversion between depth data and meters
+- Implement loop to manage all files that need to be tested
+- Implement loop to manage multiple frames from video footage
diff --git a/marshall/__pycache__/camera.cpython-310.pyc b/marshall/__pycache__/camera.cpython-310.pyc
new file mode 100644
index 0000000..c2d4762
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diff --git a/marshall/__pycache__/curve_fitting.cpython-310.pyc b/marshall/__pycache__/curve_fitting.cpython-310.pyc
new file mode 100644
index 0000000..1109697
Binary files /dev/null and b/marshall/__pycache__/curve_fitting.cpython-310.pyc differ
diff --git a/marshall/__pycache__/params.cpython-310.pyc b/marshall/__pycache__/params.cpython-310.pyc
new file mode 100644
index 0000000..c9d362c
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diff --git a/marshall/build/.built_by b/marshall/build/.built_by
new file mode 100644
index 0000000..06e74ac
--- /dev/null
+++ b/marshall/build/.built_by
@@ -0,0 +1 @@
+colcon
diff --git a/marshall/build/COLCON_IGNORE b/marshall/build/COLCON_IGNORE
new file mode 100644
index 0000000..e69de29
diff --git a/marshall/camera.py b/marshall/camera.py
new file mode 100644
index 0000000..9bd20e4
--- /dev/null
+++ b/marshall/camera.py
@@ -0,0 +1,280 @@
+import copy
+import cv2
+import numpy
+import math
+from skimage import io
+
+def mkmat(rows, cols, L):
+    mat = numpy.matrix(L, dtype='float64')
+    mat.resize((rows,cols))
+    return mat
+
+
+class PinholeCameraModel:
+
+    """
+    A pinhole camera is an idealized monocular camera.
+    """
+
+    def __init__(self):
+        self.K = None
+        self.D = None
+        self.R = None
+        self.P = None
+        self.full_K = None
+        self.full_P = None
+        self.width = None
+        self.height = None
+        self.binning_x = None
+        self.binning_y = None
+        self.raw_roi = None
+        self.tf_frame = None
+        self.stamp = None
+
+    def fromCameraInfo(self, msg):
+        """
+        :param msg: camera parameters
+        :type msg:  sensor_msgs.msg.CameraInfo
+
+        Set the camera parameters from the :class:`sensor_msgs.msg.CameraInfo` message.
+        """
+        self.K = mkmat(3, 3, msg.k)
+        if msg.d:
+            self.D = mkmat(len(msg.d), 1, msg.d)
+        else:
+            self.D = None
+        self.R = mkmat(3, 3, msg.r)
+        self.P = mkmat(3, 4, msg.p)
+        self.full_K = mkmat(3, 3, msg.k)
+        self.full_P = mkmat(3, 4, msg.p)
+        self.width = msg.width
+        self.height = msg.height
+        self.binning_x = max(1, msg.binning_x)
+        self.binning_y = max(1, msg.binning_y)
+        self.resolution = (msg.width, msg.height)
+
+        self.raw_roi = copy.copy(msg.roi)
+        # ROI all zeros is considered the same as full resolution
+        if (self.raw_roi.x_offset == 0 and self.raw_roi.y_offset == 0 and
+            self.raw_roi.width == 0 and self.raw_roi.height == 0):
+            self.raw_roi.width = self.width
+            self.raw_roi.height = self.height
+
+        # Adjust K and P for binning and ROI
+        self.K[0,0] /= self.binning_x
+        self.K[1,1] /= self.binning_y
+        self.K[0,2] = (self.K[0,2] - self.raw_roi.x_offset) / self.binning_x
+        self.K[1,2] = (self.K[1,2] - self.raw_roi.y_offset) / self.binning_y
+        self.P[0,0] /= self.binning_x
+        self.P[1,1] /= self.binning_y
+        self.P[0,2] = (self.P[0,2] - self.raw_roi.x_offset) / self.binning_x
+        self.P[1,2] = (self.P[1,2] - self.raw_roi.y_offset) / self.binning_y
+
+    def to_npz(self, output_path):
+        attribs = ['K', 'D', 'R', 'P', 'full_K', 'full_P', 'width', 'height', 'binning_x', 'binning_y',
+                   'resolution']
+        vals = {attrib: getattr(self, attrib) for attrib in attribs}
+        numpy.savez(output_path, **vals)
+
+    def from_npz(self, path):
+        for attrib, val in numpy.load(path).items():
+            setattr(self, attrib, val)
+
+    def rectifyImage(self, raw, rectified):
+        """
+        :param raw:       input image
+        :type raw:        :class:`CvMat` or :class:`IplImage`
+        :param rectified: rectified output image
+        :type rectified:  :class:`CvMat` or :class:`IplImage`
+
+        Applies the rectification specified by camera parameters :math:`K` and and :math:`D` to image `raw` and writes the resulting image `rectified`.
+        """
+
+        self.mapx = numpy.ndarray(shape=(self.height, self.width, 1),
+                           dtype='float32')
+        self.mapy = numpy.ndarray(shape=(self.height, self.width, 1),
+                           dtype='float32')
+        cv2.initUndistortRectifyMap(self.K, self.D, self.R, self.P,
+                (self.width, self.height), cv2.CV_32FC1, self.mapx, self.mapy)
+        cv2.remap(raw, self.mapx, self.mapy, cv2.INTER_CUBIC, rectified)
+
+    def rectifyPoint(self, uv_raw):
+        """
+        :param uv_raw:    pixel coordinates
+        :type uv_raw:     (u, v)
+
+        Applies the rectification specified by camera parameters
+        :math:`K` and and :math:`D` to point (u, v) and returns the
+        pixel coordinates of the rectified point.
+        """
+
+        src = mkmat(1, 2, list(uv_raw))
+        src.resize((1,1,2))
+        dst = cv2.undistortPoints(src, self.K, self.D, R=self.R, P=self.P)
+        return dst[0,0]
+
+    def project3dToPixel(self, point):
+        """
+        :param point:     3D point
+        :type point:      (x, y, z)
+
+        Returns the rectified pixel coordinates (u, v) of the 3D point,
+        using the camera :math:`P` matrix.
+        This is the inverse of :meth:`projectPixelTo3dRay`.
+        """
+        src = mkmat(4, 1, [point[0], point[1], point[2], 1.0])
+        dst = self.P * src
+        x = dst[0,0]
+        y = dst[1,0]
+        w = dst[2,0]
+        if w != 0:
+            return (x / w, y / w)
+        else:
+            return (float('nan'), float('nan'))
+
+    def projectPixelTo3dRay(self, uv):
+        """
+        :param uv:        rectified pixel coordinates
+        :type uv:         (u, v)
+
+        Returns the unit vector which passes from the camera center to through rectified pixel (u, v),
+        using the camera :math:`P` matrix.
+        This is the inverse of :meth:`project3dToPixel`.
+        """
+        x = (uv[0] - self.cx()) / self.fx()
+        y = (uv[1] - self.cy()) / self.fy()
+        norm = math.sqrt(x*x + y*y + 1)
+        x /= norm
+        y /= norm
+        z = 1.0 / norm
+        return (x, y, z)
+
+    def getDeltaU(self, deltaX, Z):
+        """
+        :param deltaX:          delta X, in cartesian space
+        :type deltaX:           float
+        :param Z:               Z, in cartesian space
+        :type Z:                float
+        :rtype:                 float
+
+        Compute delta u, given Z and delta X in Cartesian space.
+        For given Z, this is the inverse of :meth:`getDeltaX`.
+        """
+        fx = self.P[0, 0]
+        if Z == 0:
+            return float('inf')
+        else:
+            return fx * deltaX / Z
+
+    def getDeltaV(self, deltaY, Z):
+        """
+        :param deltaY:          delta Y, in cartesian space
+        :type deltaY:           float
+        :param Z:               Z, in cartesian space
+        :type Z:                float
+        :rtype:                 float
+
+        Compute delta v, given Z and delta Y in Cartesian space.
+        For given Z, this is the inverse of :meth:`getDeltaY`.
+        """
+        fy = self.P[1, 1]
+        if Z == 0:
+            return float('inf')
+        else:
+            return fy * deltaY / Z
+
+    def getDeltaX(self, deltaU, Z):
+        """
+        :param deltaU:          delta u in pixels
+        :type deltaU:           float
+        :param Z:               Z, in cartesian space
+        :type Z:                float
+        :rtype:                 float
+
+        Compute delta X, given Z in cartesian space and delta u in pixels.
+        For given Z, this is the inverse of :meth:`getDeltaU`.
+        """
+        fx = self.P[0, 0]
+        return Z * deltaU / fx
+
+    def getDeltaY(self, deltaV, Z):
+        """
+        :param deltaV:          delta v in pixels
+        :type deltaV:           float
+        :param Z:               Z, in cartesian space
+        :type Z:                float
+        :rtype:                 float
+
+        Compute delta Y, given Z in cartesian space and delta v in pixels.
+        For given Z, this is the inverse of :meth:`getDeltaV`.
+        """
+        fy = self.P[1, 1]
+        return Z * deltaV / fy
+
+    def fullResolution(self):
+        """Returns the full resolution of the camera"""
+        return self.resolution
+
+    def intrinsicMatrix(self):
+        """ Returns :math:`K`, also called camera_matrix in cv docs """
+        return self.K
+    def distortionCoeffs(self):
+        """ Returns :math:`D` """
+        return self.D
+    def rotationMatrix(self):
+        """ Returns :math:`R` """
+        return self.R
+    def projectionMatrix(self):
+        """ Returns :math:`P` """
+        return self.P
+    def fullIntrinsicMatrix(self):
+        """ Return the original camera matrix for full resolution """
+        return self.full_K
+    def fullProjectionMatrix(self):
+        """ Return the projection matrix for full resolution """
+        return self.full_P
+
+    def cx(self):
+        """ Returns x center """
+        return self.P[0,2]
+    def cy(self):
+        """ Returns y center """
+        return self.P[1,2]
+    def fx(self):
+        """ Returns x focal length """
+        return self.P[0,0]
+    def fy(self):
+        """ Returns y focal length """
+        return self.P[1,1]
+
+    def Tx(self):
+        """ Return the x-translation term of the projection matrix """
+        return self.P[0,3]
+
+    def Ty(self):
+        """ Return the y-translation term of the projection matrix """
+        return self.P[1,3]
+
+    def tfFrame(self):
+        """ Returns the tf frame name - a string - of the camera.
+        This is the frame of the :class:`sensor_msgs.msg.CameraInfo` message.
+        """
+        return self.tf_frame
+
+
+
+
+# IGNORE THIS STUFF
+def run_test_node():
+    import rclpy
+    from follow_the_leader.utils.ros_utils import TFNode
+    import pickle
+    class Temp(TFNode):
+        def _handle_cam_info(self, msg):
+            cam = PinholeCameraModel()
+            cam.fromCameraInfo(msg)
+            cam.to_npz('D435_640x480.camera.npz')
+    rclpy.init()
+    bla = Temp('temp', cam_info_topic='/camera/color/camera_info')
+    rclpy.spin(bla)
+    
diff --git a/marshall/connection_test.py b/marshall/connection_test.py
new file mode 100644
index 0000000..0b45dd7
--- /dev/null
+++ b/marshall/connection_test.py
@@ -0,0 +1,341 @@
+import cv2
+import math
+import params as p
+import camera as c
+import numpy as np
+import sys
+import random
+from pyk4a import PyK4APlayback
+import curve_fitting as cf
+import matplotlib.pyplot as plt
+from skimage import io, color, img_as_bool
+from curve_fitting import BezierBasedDetection, Bezier
+#from generate_3d import Generate_3D
+sys.path.insert(1, '../')
+import bezier_cyl_3d as bc3
+
+class Depths_Average:
+    """
+    Parameters:
+        depth_img: Currently uses a frame from Envy orchard, the depth image of a single tree.
+        bin_msk: Binary mask of a tree, corresponds with depth data.
+    selected_end_pointiables:
+        my_mask: reads binary mask
+        my_depth: reads depth image using skimage, which gets the depth values of the image
+        lined_mask: commented, used for visualization
+        radii: radii of branch at evaluated points along curve
+        curve_pts: evaluated points along Bezier curve
+        
+    """
+
+    def __init__(self, bin_msk):
+        self.my_mask = np.asarray(img_as_bool(cv2.resize(color.rgb2gray(cv2.imread(bin_msk).astype('uint8')),(640,576))))
+        self.my_mask2 = np.asarray(cv2.resize(color.rgb2gray(cv2.imread(bin_msk).astype('uint8')),(640,576)))
+        k4a = PyK4APlayback(p.video_file)    #specify video file you wish to open in params
+        k4a.open()
+        capture = k4a.get_next_capture()
+        self.my_depth = capture.depth
+        self.lined_mask = None
+        self.radii = None
+        self.curve_pts = None
+
+    def get_radii(self):
+        """
+        Uses curve_fitting to get Bezier curve by first fitting a curve and then determining radii along evaluated points.
+        Currently evaluates for 11 points. Returns radii, points along the curve, the curve object, and the "t" values.
+        """
+        detector = cf.BezierBasedDetection(self.my_mask, use_medial_axis=True)
+        curve = detector.fit()
+        radius_interpolator = detector.get_radius_interpolator_on_path()
+        ds = np.linspace(0, 1, p.num_cyl)
+        self.radii = radius_interpolator(ds)
+        self.curve_pts, ts = curve.eval_by_arclen(ds, normalized=True)
+        
+        return self.radii, self.curve_pts, curve, ts
+
+    def find_average(self):
+        """
+        Finds the average depth across a rectangular contour. Returns array of average depths and pixel width of tree.
+        """
+        depths = []
+        depths_average = []
+
+        for i in range(len(self.curve_pts) - 1):
+            right_bottom_pt = (
+            self.curve_pts[i][0].astype(int) + (self.radii[i]/2).astype(int), self.curve_pts[i][1].astype(int))
+            left_bottom_point = (
+            self.curve_pts[i][0].astype(int) - (self.radii[i]/2).astype(int), self.curve_pts[i][1].astype(int))
+            right_top_point = (
+            self.curve_pts[i + 1][0].astype(int) + (self.radii[i + 1]/2).astype(int), self.curve_pts[i + 1][1].astype(int))
+            left_top_pt = (
+            self.curve_pts[i + 1][0].astype(int) - (self.radii[i + 1]/2).astype(int), self.curve_pts[i + 1][1].astype(int))
+
+            arr = np.array([right_bottom_pt, left_bottom_point, left_top_pt, right_top_point])
+            img = cv2.cvtColor((self.my_mask2.copy().astype('uint8')), cv2.COLOR_GRAY2BGR)
+            img = cv2.drawContours(img, [arr.astype(int)], -1, color=(0,0,255), thickness=-1)
+            
+            pts = np.asarray(np.where(img == 255))
+            
+            arry=self.my_depth[pts[0],pts[1]]
+            
+            arr = arry[np.where(arry!=0)]
+            
+            depths.append(arr[~np.isnan(arr).any(axis=0) and arr<10000])
+            
+            ar2 = (np.mean(depths[i]))*0.0001    #need to figure out the correct conversion between depth data and meters
+            if np.isnan(ar2):    #replaces empty array values with 0
+                depths_average.append(p.nan_value)
+            else:
+                depths_average.append(ar2)
+            
+        return depths_average, self.radii
+
+
+class Determine_Match:
+    """
+    Determines if a side branch matches a leader branch.
+    """
+    def __init__(self):
+        self.angle_limit = p.angle_limit
+        
+    def return_closest(self, curve_pts, end_pt_1, end_pt_2):
+        """
+        Returns the closest distance between evaluated points on leader curve and end points of side branch curve.
+        Parameters:
+            curve_pts: all points evaluated on leader curve
+            end_pt_1: an end point on side branch curve
+            end_pt_2: other end point on side branch curve
+        Returns:
+            ind: index of matching points
+            selected_end_point: the matching end point
+            dist: minimum distance between selected points 
+        """
+        distance_arr = []
+        prev_dist = math.inf
+        for i, point in enumerate(curve_pts):
+            dist1 = math.dist(point, end_pt_1)
+            dist2 = math.dist(point, end_pt_2)
+
+            if dist1 <= dist2:
+                distance_arr.append(dist1)
+                if prev_dist >= dist1:
+                    ind, selected_end_point, dist = self.get_values(end_pt_1, i, dist1)
+                    
+            else:
+                distance_arr.append(dist2)
+                if prev_dist >= dist2:
+                    ind, selected_end_point, dist = self.get_values(end_pt_2, i, dist2)
+
+            prev_dist = dist
+
+        return ind, selected_end_point, dist
+        
+        
+    def get_values(self, end_point, ind, dist):
+        """
+        returns index, end_point, and dist after conditions of return_closest are satisfied
+        """
+        return ind, end_point, dist
+            
+    def depth_scoring(self, closest_depth, end_depth):
+        """
+        Parameters:
+            closest_depth: depth of closest point on leader curve
+            end_depth: depth of selected end point
+        Returns:
+            the difference between the two (the difference in depth)
+        """
+        return abs(closest_depth - end_depth)
+
+
+    def check_angle_match(self, vec_1, vec_2):
+        """
+        Checks if the angle falls within the given angle parameters.
+        Parameters:
+            vec_1: a tangent line to one of the selected points
+            vec_2: a tangent line to the other selected point
+        Returns:
+            a score based on if the angle between the two vectors falls in an acceptable range. Currently set to arbitrary numbers.
+        """
+        angle = np.arccos(
+            np.clip(np.dot((vec_1 / np.linalg.norm(vec_1)), (vec_2 / np.linalg.norm(vec_2))), -1.0, 1.0)) * (
+                            180 / np.pi)
+        
+        if angle < self.angle_limit:
+            return 1
+
+        elif angle > self.angle_limit:
+            return 0
+
+        else:
+            return 0.5
+
+
+class Build_3D:
+    """
+    Constructs 3D cylinders for a given curve
+    Parameters:
+        curve_points: given points along a Bezier curve
+        radii: radii at curve_points
+        name: whether the branch is a follower or leader
+    """
+    def __init__(self, curve_points, radii, name):
+        self.radii = radii
+        self.curve_points = curve_points
+        self.name = name
+        self.n_along = 10 * p.cyls    #parameter for faces 
+        self.n_around = 64    #parameter for faces
+        
+    def set_real_measurements(self):
+        """
+        Takes curve_points and converts to size in meters, scales up for visibility
+        """
+        camera = c.PinholeCameraModel()
+        camera.from_npz(p.cam)
+        assert isinstance(camera, c.PinholeCameraModel)
+        for i in range(len(self.curve_points)):
+            self.curve_points[i][0] = camera.getDeltaX(self.curve_points[i][0], self.curve_points[i][2])*p.scale_factor
+            self.curve_points[i][1] = camera.getDeltaY(self.curve_points[i][1], self.curve_points[i][2])*p.scale_factor
+            self.radii[i] = camera.getDeltaX(self.radii[i], self.curve_points[i][2])*p.scale_factor
+                       
+    def build(self):
+        """
+        Passes in beginning, middle, and end curve points and beginning and end radii to a class that builds a 3D mesh for each cylinder
+        merges all cylinders by altering obj files
+        """
+        self.set_real_measurements()
+        
+        for i in range(len(self.curve_points)-2):
+            b = bc3.BezierCyl3D(self.curve_points[i], self.curve_points[i+1], self.curve_points[i+2], self.radii[i], self.radii[i+2])
+            b.make_mesh()
+            b.write_mesh(f"{self.name}_{i}.obj")
+            self.write_verts(f"{self.name}_{i}.obj")
+        self.write_f()
+        self.merge_files()
+        
+    def write_verts(self, fi):
+        """
+        Passes in generated cylinder file and appends vertices to a list
+        """
+        count = 0
+        with open(fi, 'r') as f, open(f"v_lines{self.name}.obj", 'a') as vl:
+            data = f.readlines()
+            for line in data:
+                if "v" in line:
+                    vl.write(line)
+
+    def write_f(self):
+        """
+        writes faces to a file
+        """
+        with open(f"f_lines{self.name}.obj", 'w') as fl:      
+            for it in range(0, self.n_along - 1):
+                i_curr = it * self.n_around + 1
+                i_next = (it+1) * self.n_around + 1
+                for ir in range(0, self.n_around):
+                    ir_next = (ir + 1) % self.n_around
+                    fl.write(f"f {i_curr + ir} {i_next + ir_next} {i_curr + ir_next} \n")
+                    fl.write(f"f {i_curr + ir} {i_next + ir} {i_next + ir_next} \n")
+                  
+    def merge_files(self):  
+        """
+        merges object files based on faces and verts
+        """
+        with open(f"curve{self.name}.obj", 'w') as c, open(f"v_lines{self.name}.obj", 'r') as vl, open(f"f_lines{self.name}.obj", 'r') as fl:
+            file1 = vl.read()
+            file2 = fl.read()
+            c.write(file1)
+            c.write(file2)
+
+def make_tree(file1, file2):
+    """
+    constructs the tree by merging generated verticies files
+    """
+    n_along = 10 * p.cyls
+    n_around = 64
+    with open(file1, "r") as f1, open(file2, "r") as f2, open("treefile.obj", "w") as tf:
+        data1 = f1.readlines()
+        tf.writelines(data1)
+        data2 = f2.readlines()
+        tf.writelines(data2)         
+        for it in range(0, (n_along*2) - 1):
+            i_curr = it * (n_around) + 1
+            i_next = (it+1) * (n_around) + 1
+            for ir in range(0, (n_around)):
+                ir_next = (ir + 1) % (n_around)
+                tf.write(f"f {i_curr + ir} {i_next + ir_next} {i_curr + ir_next} \n")
+                tf.write(f"f {i_curr + ir} {i_next + ir} {i_next + ir_next} \n")
+                             
+def manage_arrs(curve_2d, depth_arr):
+    """
+    Splits curve_2D and depth_arr to their components, as well as merging them
+    Parameters:
+        curve_2d: 2D Bezier points in x and y from a mask
+        depth_arr: depth at those points
+    """
+    split_curve = np.split(curve_2d, 2, 1)
+    _x = np.delete(split_curve[0], -1)
+    _y = np.delete(split_curve[1], -1)
+    _z = np.asarray(depth_arr)
+    full_arr = np.array([_x, _y, _z]).T
+    
+    return _x, _y, _z, full_arr
+
+
+if __name__ == '__main__':
+
+    d = Depths_Average(p.mask_img)
+    rad, curve_pts, curve, ts = d.get_radii()
+    depth, num_pix = d.find_average()
+
+    d2 = Depths_Average(p.follower_msk)
+    rad2, curve_pts2, curve2, ts2 = d2.get_radii()
+    depth2, num_pix2 = d2.find_average()
+
+    x1, y1, z1, leader_pts = manage_arrs(curve_pts, depth)
+    x2, y2, z2, follower_pts = manage_arrs(curve_pts2, depth2)
+    
+    dm = Determine_Match()
+    
+    end1 = follower_pts[0]
+    end2 = follower_pts[-1]
+
+    index, end_pt, minimum_distance = dm.return_closest(leader_pts, end1, end2)
+    depth_score = dm.depth_scoring(z1[index], end_pt[2])
+    leader_tan = curve.tangent(ts[index])
+    follower_tan = curve2.tangent(ts2[index])
+
+    angle_score = dm.check_angle_match(leader_tan, follower_tan)
+    total_score = angle_score + depth_score + minimum_distance
+    
+    b = Build_3D(leader_pts, rad, "leader")
+    b.build()
+    
+    b2 = Build_3D(follower_pts, rad2, "follower")
+    b2.build()
+    
+    make_tree("v_linesleader.obj", "v_linesfollower.obj")
+    
+    #g2 = Generate_3D(follower_pts, x2, y2, z2, num_pix2)
+    #g2.create_mesh()
+    
+    fig = plt.figure()
+    ax = fig.add_subplot(projection='3d')
+    
+    print("Total: ", total_score)
+    print("Angle Score: ", angle_score)
+    print("Min Dist: ", minimum_distance)
+    print("Depth Difference: ", depth_score)
+    
+    #Uncomment below if you wish to visualize both curves
+    """
+    ax.scatter(x1, y1, z1)
+    ax.scatter(x2, y2, z2)
+    
+    ax.plot(x1, y1, z1)
+    ax.plot(x2, y2, z2)
+    ax.scatter(*np.asarray(end1).T)
+    ax.scatter(*np.asarray(end2).T)
+    ax.axis('equal')
+    plt.show()
+    """
diff --git a/marshall/curve_fitting.py b/marshall/curve_fitting.py
new file mode 100644
index 0000000..9f425a0
--- /dev/null
+++ b/marshall/curve_fitting.py
@@ -0,0 +1,479 @@
+import numpy as np
+import os
+from matplotlib import pyplot as plt
+from scipy.special import comb
+from skimage.morphology import skeletonize, medial_axis
+from skimage import io, img_as_bool, color
+import networkx as nx
+from scipy.spatial import KDTree
+from scipy.interpolate import interp1d
+import cv2
+
+class BezierBasedDetection:
+    def __init__(self, mask, outlier_threshold=4, use_medial_axis=False):
+        self.mask = mask
+        self.skel = None
+        self.dists = None
+        self.stats = {}
+        self.outlier_threshold = outlier_threshold
+        self.use_medial_axis = use_medial_axis
+
+        self.subsampled_graph = None
+        self.selected_path = None
+        self.selected_curve = None
+
+    def construct_skeletal_graph(self, trim=0):
+        graph = nx.Graph()
+        if self.use_medial_axis:
+            skel, dists = medial_axis(self.mask, return_distance=True)
+        else:
+            skel = skeletonize(self.mask)
+            dists = None
+
+        if trim:
+            skel[:trim] = 0
+            skel[-trim:] = 0
+            skel[:,:trim] = 0
+            skel[:,-trim:] = 0
+
+        self.skel = skel
+        self.dists = dists
+        pxs = np.array(np.where(skel)).T[:, [1, 0]]
+        for px in pxs:
+            graph.add_node(tuple(px))
+            for dir in np.array([[-1,0],[1,0],[0,1],[0,-1],[-1,-1],[-1,1],[1,-1],[1,1]]):
+                new_px = dir + px
+                if (0 <= new_px[0] < self.mask.shape[1]) and (0 <= new_px[1] < self.mask.shape[0]) and skel[new_px[1], new_px[0]]:
+                    graph.add_node(tuple(new_px))
+                    graph.add_edge(tuple(px), tuple(new_px), distance=np.linalg.norm(dir))
+
+        subgraph = nx.minimum_spanning_tree(graph.subgraph(max(nx.connected_components(graph), key=len)))
+        deg_1_nodes = [n for n, deg in subgraph.degree if deg == 1]
+
+        downsampled = nx.Graph()
+        # Process the edges to form a downsampled graph
+
+        node = deg_1_nodes[0]
+        downsampled.add_node(node)
+        path = [node]
+        for edge in nx.dfs_edges(subgraph):
+            node = path[-1]
+            if edge[0] == node:
+                path.append(edge[1])
+            else:
+                path = [edge[0], edge[1]]
+
+            if subgraph.degree(edge[1]) != 2:
+                downsampled.add_node(edge[1])
+                downsampled.add_edge(path[0], path[-1], path=path)
+                path = [edge[1]]
+
+        return downsampled
+
+    def do_curve_search(self, graph, start_nodes, min_len=0, filter_mask=None, return_stats=False):
+        most_matches = 0
+        best_curve = None
+        best_path = None
+        stats = {}
+
+        for node in start_nodes:
+
+            path_dict = {node: None}
+            def retrieve_path_pts(n):
+                edges = []
+                path = [n]
+                while path_dict[n] is not None:
+                    edges.append((path_dict[n], n))
+                    n = path_dict[n]
+                    path.append(n)
+                edges = edges[::-1]
+                path = path[::-1]
+
+                px_list = []
+                for edge in edges:
+                    px_path = graph.edges[edge]['path']
+                    if px_path[0] != edge[0]:
+                        px_path = px_path[::-1]
+                    px_list.extend(px_path)
+
+                pts = np.array(px_list)
+                return path, pts
+
+            for edge in nx.dfs_edges(graph, source=node):
+                path_dict[edge[1]] = edge[0]
+                node_path, pts = retrieve_path_pts(edge[1])
+                if filter_mask is not None:
+                    pts = pts[~filter_mask[pts[:,1], pts[:,0]]]
+                if not len(pts):
+                    continue
+                cum_dists = np.zeros(pts.shape[0])
+                offsets = np.linalg.norm(pts[1:] - pts[:-1], axis=1)
+                cum_dists[1:] = np.cumsum(offsets)
+                if cum_dists[-1] < min_len:
+                    continue
+
+                curve = Bezier.fit(pts, 3)
+                new_dists = curve.arclen * cum_dists / cum_dists[-1]
+                new_dists[-1] = curve.arclen
+                eval_bezier, _ = curve.eval_by_arclen(new_dists)
+                matched_pts = np.linalg.norm(pts - eval_bezier, axis=1) < self.outlier_threshold
+                matches = matched_pts.sum()
+
+                if matches > most_matches:
+                    most_matches = matches
+                    best_curve = curve
+                    best_path = node_path
+                    stats = {
+                        'pts': pts,
+                        'matched_idx': matched_pts,
+                        'matches': matches,
+                        'consistency': matched_pts.mean(),
+                    }
+
+        if return_stats:
+            return best_curve, best_path, stats
+
+        return best_curve, best_path
+
+    def fit(self, vec=None, trim=30):
+
+        if vec is None:
+            # Run SVD to find the most significant direction
+            pxs = np.fliplr(np.array(np.where(self.mask)).T)
+            pxs = pxs - pxs.mean(axis=0)
+            # SVD takes a lot of memory - we subsample points as we only need an estimate
+            pxs = pxs[np.random.choice(len(pxs), 100, replace=False)]
+            u, s, v = np.linalg.svd(pxs, full_matrices=True)
+            
+        vec = (0,1)
+        #vec = np.array(vec) / np.linalg.norm(vec)
+        # Iterate through the edges and use the vec to determine the orientation
+
+        graph = self.construct_skeletal_graph(trim=trim)
+        directed_graph = nx.DiGraph()
+        directed_graph.add_nodes_from(graph.nodes)
+
+        for p1, p2 in graph.edges:
+            path = graph.edges[p1, p2]['path']
+            if np.dot(np.array(p2) - p1, vec) < 0:
+                p1, p2 = p2, p1
+            if path[0] != p1:
+                path = path[::-1]
+            directed_graph.add_edge(p1, p2, path=path)
+
+        start_nodes = [n for n in graph.nodes if directed_graph.out_degree(n) == 1 and directed_graph.in_degree(n) == 0]
+        best_curve, best_path, stats = self.do_curve_search(directed_graph, start_nodes, return_stats=True)
+
+        self.subsampled_graph = graph
+        self.selected_path = best_path
+        self.selected_curve = best_curve
+        self.stats = stats
+
+        return best_curve
+
+    def run_side_branch_search(self, min_len=80, filter_mask=None, visualize=''):
+        if self.selected_path is None:
+            raise Exception('Please run the fit function first')
+
+        graph = self.subsampled_graph
+        assert isinstance(graph, nx.Graph)
+
+        # Subgraph pre-processing
+        main_path = self.selected_path
+        for edge in zip(main_path[:-1], main_path[1:]):
+            graph.remove_edge(*edge)
+
+        candidate_edges = []
+        to_remove = []
+        for i, node in enumerate(main_path):
+
+            for neighbor in graph[node]:
+                edge = (node, neighbor)
+                path = graph.edges[edge]['path']
+                if path[0] != node:
+                    path = path[::-1]       # Orient the path from the main branch outwards
+
+                to_remove.append(edge)
+                if 0 < i < len(main_path) - 1:
+                    candidate_edges.append((edge, path))
+
+        graph.remove_edges_from(to_remove)
+
+        side_branches = []
+        stats = []
+        for candidate_edge, path in candidate_edges:
+            graph.add_edge(*candidate_edge, path=path)
+
+            best_curve, best_path, match_stats = self.do_curve_search(graph, start_nodes=[candidate_edge[0]],
+                                                                      min_len=min_len, filter_mask=filter_mask,
+                                                                      return_stats=True)
+            if best_curve is not None:
+                info = {'curve': best_curve, 'path': best_path, 'stats': match_stats}
+                side_branches.append(info)
+                if visualize:
+                    stats.append(match_stats)
+
+            graph.remove_edge(*candidate_edge)
+
+        if visualize:
+            import cv2
+            from PIL import Image
+
+            base_img = np.dstack([self.mask * 255] * 3).astype(np.uint8)
+            ts = np.linspace(0, 1, 201)
+            eval_bezier = self.selected_curve(ts)
+
+            cv2.polylines(base_img, [eval_bezier.reshape((-1, 1, 2)).astype(int)], False, (0, 0, 255), 4)
+            for info, stat in zip(side_branches, stats):
+
+                curve = info['curve']
+                eval_bezier = curve(ts)
+                msg = 'Matches: {}, {:.1f}%'.format(stat['matches'], stat['consistency'] * 100)
+                cv2.polylines(base_img, [eval_bezier.reshape((-1, 1, 2)).astype(int)], False, (0, 128, 0), 4)
+                draw_pt = eval_bezier[len(eval_bezier) // 2].astype(int)
+                text_size = cv2.getTextSize(msg, cv2.FONT_HERSHEY_SIMPLEX, 0.5, 2)[0]
+                if draw_pt[0] + text_size[0] > base_img.shape[1]:
+                    draw_pt[0] -= text_size[1]
+
+                cv2.putText(base_img, msg, draw_pt, cv2.FONT_HERSHEY_SIMPLEX, 0.5, (255, 0, 255), 2)
+
+            Image.fromarray(base_img).save(visualize)
+
+        return side_branches
+
+    def get_radius_interpolator_on_path(self, path=None, min_quant=0.25, max_quant=0.75):
+        if self.dists is None:
+            raise Exception('Please run the medial axis transform before running this function')
+
+        if path is None:
+            path = self.stats['pts']
+
+        radii = self.dists[path[:,1], path[:,0]].copy()
+        if 0 in radii:
+            raise Exception('Some pixels in the specified path were not part of the skeleton!')
+        q_min = np.quantile(radii, min_quant)
+        q_max = np.quantile(radii, max_quant)
+        min_bound = q_min - min_quant * (q_max - q_min) / (max_quant - min_quant)
+        max_bound = q_max + max_quant * (q_max - q_min) / (max_quant - min_quant)
+        radii[(radii < min_bound) | (radii > max_bound)] = np.median(radii)
+
+        cum_dists = np.zeros(len(path))
+        cum_dists[1:] = np.linalg.norm(path[1:] - path[:-1], axis=1).cumsum()
+        cum_dists /= cum_dists[-1]
+
+        return interp1d(cum_dists, radii)
+
+
+
+class Bezier:
+    # https://stackoverflow.com/questions/12643079/b%c3%a9zier-curve-fitting-with-scipy
+
+    def __init__(self, ctrl_pts, approx_eval=201):
+        self.pts = ctrl_pts
+        self.approx_eval = approx_eval
+        self._kd_tree = None
+        self._ts = None
+
+        # Arc length-based interpolation tools
+        self._len_approx = None
+        self._dist_t_interpolator = None
+        self._t_dist_interpolator = None
+
+    @property
+    def n(self):
+        return len(self.pts)
+
+    @property
+    def deg(self):
+        return len(self.pts) - 1
+
+    @staticmethod
+    def bpoly(i, n, t):
+        return comb(n, i) * t ** (n-i) * (1 - t) ** i
+
+    def __call__(self, t):
+        t = np.array(t)
+        polys = [self.bpoly(i, self.deg, t)[..., np.newaxis] * pt for i, pt in enumerate(self.pts)]
+        return np.sum(polys, axis=0)
+
+    def _load_arclen_tools(self):
+        if self._len_approx is not None:
+            return
+        ts_approx = np.linspace(0, 1, self.approx_eval)
+        eval_pts = self(ts_approx)
+        cum_dists = np.zeros(self.approx_eval)
+        cum_dists[1:] = np.linalg.norm(eval_pts[:-1] - eval_pts[1:], axis=1).cumsum()
+        self._len_approx = cum_dists[-1]
+
+        self._dist_t_interpolator = interp1d(cum_dists, ts_approx)
+        self._t_dist_interpolator = interp1d(ts_approx, cum_dists)
+
+    @property
+    def arclen(self):
+        self._load_arclen_tools()
+        return self._len_approx
+
+    def eval_by_arclen(self, dists, normalized=False):
+        # Evaluates the curve, but with the ts parametrized by the distance along the curve (using an approximation)
+        self._load_arclen_tools()
+        if normalized:
+            dists = np.array(dists) * self.arclen
+        ts = self._dist_t_interpolator(dists)
+        return self(ts), ts
+
+    def t_to_curve_dist(self, ts):
+        self._load_arclen_tools()
+        return self._t_dist_interpolator(ts)
+
+    def tangent(self, t):
+        t = np.array(t)
+        polys = [self.deg * self.bpoly(i, self.deg - 1, t)[..., np.newaxis] * (p2 - p1)
+                 for i, (p1, p2) in enumerate(zip(self.pts[:-1], self.pts[1:]))]
+        return -np.sum(polys, axis=0)
+
+    def visualize(self, other_pts=None):
+        eval_pts = self(np.linspace(0, 1, 100))
+        if other_pts is not None:
+            plt.scatter(*other_pts.T, color='grey', marker='x', s=3)
+        plt.scatter(*self.pts.T, color='red', marker='*', s=10)
+        plt.scatter(*eval_pts.T, color='blue', s=5)
+        plt.show()
+
+    @classmethod
+    def fit(cls, pts, degree=3):
+        # Assumes pts[0] and pts[-1] represent the respective endpoints of the Bezier curve
+        n = len(pts)
+        t = np.linspace(0, 1, n)
+        b_mat = np.array([cls.bpoly(i, degree, t) for i in range(degree+1)]).T
+        fit = np.linalg.pinv(b_mat) @ pts
+        return cls(fit)
+
+    @classmethod
+    def iterative_fit(cls, pts, degree=3, inlier_threshold=0.05, resample_p=0.5, exclude_furthest=0.10,
+                      max_iters=10, stop_threshold=0.75):
+        """
+        Attempts to fit a Bezier curve to noisy data by with a RANSAC-like approach.
+        Iteratively estimates a model, identifies inliers, and reestimates the model until the desired number of
+        inliers has been met.
+        inlier_threshold: Distance from point to curve to be considered an inlier
+        resample_p: Proportion of points that are resampled to fit a new model
+        exclude_furthest: This proportion of points furthest from the current model will not be considered for model fitting
+        stop_threshold: Process terminates once this proportion of inliers has been met
+        """
+
+        stats = {
+            'success': False,
+            'iters': 0,
+            'inliers': 0,
+            'inlier_idx': [],
+            'init_inliers': 0,
+        }
+
+        current_model = cls.fit(pts, degree=degree)
+        best_model = None
+        best_inlier_p = 0.0
+
+        for i in range(max_iters):
+            stats['iters'] += 1
+            dists, _ = current_model.query_pt_distance(pts)
+            inliers = dists < inlier_threshold
+            inlier_p = inliers.mean()
+            stats['inliers'] = inlier_p
+            if i == 0:
+                stats['init_inliers'] = inlier_p
+
+            if inlier_p > best_inlier_p:
+                best_model = current_model
+                best_inlier_p = inlier_p
+                stats['inlier_idx'] = inliers
+
+            if inlier_p >= stop_threshold:
+                stats['success'] = True
+                return current_model, stats
+
+            # Using the current model, exclude the furthest points and subsample a new selection of points
+            eligible = np.argsort(dists)[:int((1-exclude_furthest) * len(pts))]
+            to_sample = np.random.choice(eligible, int(resample_p * len(pts)), replace=False)
+            to_use = np.zeros(len(pts), dtype=bool)
+            to_use[0] = to_use[-1] = True
+            to_use[to_sample] = True
+            current_model = cls.fit(pts[to_use])
+
+        print('Warning: Iterative fit maxed out!')
+        return best_model, stats
+
+    def query_pt_distance(self, pts):
+
+        if self._kd_tree is None:
+            self._ts = np.linspace(0, 1, self.approx_eval, endpoint=True)
+            curve_eval = self(self._ts)
+            self._kd_tree = KDTree(curve_eval)
+
+        dists, idxs = self._kd_tree.query(pts)
+        return dists, self._ts[idxs]
+
+
+# TESTS
+def side_branch_test():
+    from PIL import Image
+    import cv2
+
+
+    proc_dir = os.path.join(os.path.expanduser('~'), 'Pictures', 'masks')
+    output_dir = os.path.join(proc_dir, 'outputs')
+    files = [x for x in os.listdir(proc_dir) if x.endswith('.png')]
+
+    for file in files:
+        input_file = os.path.join(proc_dir, file)
+        output_file = os.path.join(output_dir, file)
+        img = np.array(Image.open(input_file))[:, :, :3].copy()
+        mask = img.mean(axis=2) > 128
+
+        detection = BezierBasedDetection(mask, outlier_threshold=6, use_medial_axis=True)
+        curve = detection.fit(vec=(0, -1))
+        if curve is None:
+            continue
+
+        radius_interpolator = detection.get_radius_interpolator_on_path()
+        detection.run_side_branch_search(visualize=output_file, min_len=40, radius_interpolator=radius_interpolator)
+
+
+def ransac_fit_test():
+
+    import matplotlib.pyplot as plt
+    import time
+
+    for _ in range(100):
+        rand_pts = np.random.uniform(-1, 1, (4,3))
+        curve = Bezier(rand_pts)
+        num_ts = np.random.randint(10, 50)
+        ts = np.random.uniform(0, 1, num_ts)
+        ts.sort()
+
+        vals = curve(ts) + np.random.uniform(-0.01, 0.01, (num_ts, 3))
+
+        super_noisy_pts = int(np.random.uniform(0.1, 0.2) * num_ts)
+        idxs_to_modify = np.random.choice(num_ts - 2, super_noisy_pts, replace=False) + 1       # Don't modify the start/end points
+        vals[idxs_to_modify] += np.random.uniform(-2.0, 2.0, (super_noisy_pts, 3))
+
+        start = time.time()
+        fit_curve, stats = Bezier.iterative_fit(vals, max_iters=100)
+        end = time.time()
+
+        print('Fit of {} points took {:.3f}s ({} iters)'.format(num_ts, end-start, stats['iters']))
+        print('Percent inliers: {:.2f}% (init {:.2f}%)'.format(stats['inliers'] * 100, stats['init_inliers'] * 100))
+
+        ax = plt.figure().add_subplot(projection='3d')
+
+        ts = np.linspace(0, 1, 51)
+        real_pts = curve(ts)
+        est_pts = fit_curve(ts)
+        naive_pts = Bezier.fit(vals)(ts)
+
+        ax.plot(*real_pts.T, color='green', linestyle='dashed')
+        ax.plot(*est_pts.T, color='blue')
+        ax.plot(*naive_pts.T, color='red', linestyle='dotted')
+        ax.scatter(*vals[stats['inlier_idx']].T, color='green')
+        ax.scatter(*vals[~stats['inlier_idx']].T, color='red')
+
+        plt.show()
diff --git a/marshall/follower_mask.png b/marshall/follower_mask.png
new file mode 100644
index 0000000..727cdc2
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diff --git a/marshall/generated.png b/marshall/generated.png
new file mode 100644
index 0000000..a2edaf7
Binary files /dev/null and b/marshall/generated.png differ
diff --git a/marshall/generated_tree.png b/marshall/generated_tree.png
new file mode 100644
index 0000000..79a810a
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diff --git a/marshall/install/.colcon_install_layout b/marshall/install/.colcon_install_layout
new file mode 100644
index 0000000..3aad533
--- /dev/null
+++ b/marshall/install/.colcon_install_layout
@@ -0,0 +1 @@
+isolated
diff --git a/marshall/install/COLCON_IGNORE b/marshall/install/COLCON_IGNORE
new file mode 100644
index 0000000..e69de29
diff --git a/marshall/install/_local_setup_util_ps1.py b/marshall/install/_local_setup_util_ps1.py
new file mode 100644
index 0000000..98348ee
--- /dev/null
+++ b/marshall/install/_local_setup_util_ps1.py
@@ -0,0 +1,404 @@
+# Copyright 2016-2019 Dirk Thomas
+# Licensed under the Apache License, Version 2.0
+
+import argparse
+from collections import OrderedDict
+import os
+from pathlib import Path
+import sys
+
+
+FORMAT_STR_COMMENT_LINE = '# {comment}'
+FORMAT_STR_SET_ENV_VAR = 'Set-Item -Path "Env:{name}" -Value "{value}"'
+FORMAT_STR_USE_ENV_VAR = '$env:{name}'
+FORMAT_STR_INVOKE_SCRIPT = '_colcon_prefix_powershell_source_script "{script_path}"'
+FORMAT_STR_REMOVE_LEADING_SEPARATOR = ''
+FORMAT_STR_REMOVE_TRAILING_SEPARATOR = ''
+
+DSV_TYPE_APPEND_NON_DUPLICATE = 'append-non-duplicate'
+DSV_TYPE_PREPEND_NON_DUPLICATE = 'prepend-non-duplicate'
+DSV_TYPE_PREPEND_NON_DUPLICATE_IF_EXISTS = 'prepend-non-duplicate-if-exists'
+DSV_TYPE_SET = 'set'
+DSV_TYPE_SET_IF_UNSET = 'set-if-unset'
+DSV_TYPE_SOURCE = 'source'
+
+
+def main(argv=sys.argv[1:]):  # noqa: D103
+    parser = argparse.ArgumentParser(
+        description='Output shell commands for the packages in topological '
+                    'order')
+    parser.add_argument(
+        'primary_extension',
+        help='The file extension of the primary shell')
+    parser.add_argument(
+        'additional_extension', nargs='?',
+        help='The additional file extension to be considered')
+    parser.add_argument(
+        '--merged-install', action='store_true',
+        help='All install prefixes are merged into a single location')
+    args = parser.parse_args(argv)
+
+    packages = get_packages(Path(__file__).parent, args.merged_install)
+
+    ordered_packages = order_packages(packages)
+    for pkg_name in ordered_packages:
+        if _include_comments():
+            print(
+                FORMAT_STR_COMMENT_LINE.format_map(
+                    {'comment': 'Package: ' + pkg_name}))
+        prefix = os.path.abspath(os.path.dirname(__file__))
+        if not args.merged_install:
+            prefix = os.path.join(prefix, pkg_name)
+        for line in get_commands(
+            pkg_name, prefix, args.primary_extension,
+            args.additional_extension
+        ):
+            print(line)
+
+    for line in _remove_ending_separators():
+        print(line)
+
+
+def get_packages(prefix_path, merged_install):
+    """
+    Find packages based on colcon-specific files created during installation.
+
+    :param Path prefix_path: The install prefix path of all packages
+    :param bool merged_install: The flag if the packages are all installed
+      directly in the prefix or if each package is installed in a subdirectory
+      named after the package
+    :returns: A mapping from the package name to the set of runtime
+      dependencies
+    :rtype: dict
+    """
+    packages = {}
+    # since importing colcon_core isn't feasible here the following constant
+    # must match colcon_core.location.get_relative_package_index_path()
+    subdirectory = 'share/colcon-core/packages'
+    if merged_install:
+        # return if workspace is empty
+        if not (prefix_path / subdirectory).is_dir():
+            return packages
+        # find all files in the subdirectory
+        for p in (prefix_path / subdirectory).iterdir():
+            if not p.is_file():
+                continue
+            if p.name.startswith('.'):
+                continue
+            add_package_runtime_dependencies(p, packages)
+    else:
+        # for each subdirectory look for the package specific file
+        for p in prefix_path.iterdir():
+            if not p.is_dir():
+                continue
+            if p.name.startswith('.'):
+                continue
+            p = p / subdirectory / p.name
+            if p.is_file():
+                add_package_runtime_dependencies(p, packages)
+
+    # remove unknown dependencies
+    pkg_names = set(packages.keys())
+    for k in packages.keys():
+        packages[k] = {d for d in packages[k] if d in pkg_names}
+
+    return packages
+
+
+def add_package_runtime_dependencies(path, packages):
+    """
+    Check the path and if it exists extract the packages runtime dependencies.
+
+    :param Path path: The resource file containing the runtime dependencies
+    :param dict packages: A mapping from package names to the sets of runtime
+      dependencies to add to
+    """
+    content = path.read_text()
+    dependencies = set(content.split(os.pathsep) if content else [])
+    packages[path.name] = dependencies
+
+
+def order_packages(packages):
+    """
+    Order packages topologically.
+
+    :param dict packages: A mapping from package name to the set of runtime
+      dependencies
+    :returns: The package names
+    :rtype: list
+    """
+    # select packages with no dependencies in alphabetical order
+    to_be_ordered = list(packages.keys())
+    ordered = []
+    while to_be_ordered:
+        pkg_names_without_deps = [
+            name for name in to_be_ordered if not packages[name]]
+        if not pkg_names_without_deps:
+            reduce_cycle_set(packages)
+            raise RuntimeError(
+                'Circular dependency between: ' + ', '.join(sorted(packages)))
+        pkg_names_without_deps.sort()
+        pkg_name = pkg_names_without_deps[0]
+        to_be_ordered.remove(pkg_name)
+        ordered.append(pkg_name)
+        # remove item from dependency lists
+        for k in list(packages.keys()):
+            if pkg_name in packages[k]:
+                packages[k].remove(pkg_name)
+    return ordered
+
+
+def reduce_cycle_set(packages):
+    """
+    Reduce the set of packages to the ones part of the circular dependency.
+
+    :param dict packages: A mapping from package name to the set of runtime
+      dependencies which is modified in place
+    """
+    last_depended = None
+    while len(packages) > 0:
+        # get all remaining dependencies
+        depended = set()
+        for pkg_name, dependencies in packages.items():
+            depended = depended.union(dependencies)
+        # remove all packages which are not dependent on
+        for name in list(packages.keys()):
+            if name not in depended:
+                del packages[name]
+        if last_depended:
+            # if remaining packages haven't changed return them
+            if last_depended == depended:
+                return packages.keys()
+        # otherwise reduce again
+        last_depended = depended
+
+
+def _include_comments():
+    # skipping comment lines when COLCON_TRACE is not set speeds up the
+    # processing especially on Windows
+    return bool(os.environ.get('COLCON_TRACE'))
+
+
+def get_commands(pkg_name, prefix, primary_extension, additional_extension):
+    commands = []
+    package_dsv_path = os.path.join(prefix, 'share', pkg_name, 'package.dsv')
+    if os.path.exists(package_dsv_path):
+        commands += process_dsv_file(
+            package_dsv_path, prefix, primary_extension, additional_extension)
+    return commands
+
+
+def process_dsv_file(
+    dsv_path, prefix, primary_extension=None, additional_extension=None
+):
+    commands = []
+    if _include_comments():
+        commands.append(FORMAT_STR_COMMENT_LINE.format_map({'comment': dsv_path}))
+    with open(dsv_path, 'r') as h:
+        content = h.read()
+    lines = content.splitlines()
+
+    basenames = OrderedDict()
+    for i, line in enumerate(lines):
+        # skip over empty or whitespace-only lines
+        if not line.strip():
+            continue
+        try:
+            type_, remainder = line.split(';', 1)
+        except ValueError:
+            raise RuntimeError(
+                "Line %d in '%s' doesn't contain a semicolon separating the "
+                'type from the arguments' % (i + 1, dsv_path))
+        if type_ != DSV_TYPE_SOURCE:
+            # handle non-source lines
+            try:
+                commands += handle_dsv_types_except_source(
+                    type_, remainder, prefix)
+            except RuntimeError as e:
+                raise RuntimeError(
+                    "Line %d in '%s' %s" % (i + 1, dsv_path, e)) from e
+        else:
+            # group remaining source lines by basename
+            path_without_ext, ext = os.path.splitext(remainder)
+            if path_without_ext not in basenames:
+                basenames[path_without_ext] = set()
+            assert ext.startswith('.')
+            ext = ext[1:]
+            if ext in (primary_extension, additional_extension):
+                basenames[path_without_ext].add(ext)
+
+    # add the dsv extension to each basename if the file exists
+    for basename, extensions in basenames.items():
+        if not os.path.isabs(basename):
+            basename = os.path.join(prefix, basename)
+        if os.path.exists(basename + '.dsv'):
+            extensions.add('dsv')
+
+    for basename, extensions in basenames.items():
+        if not os.path.isabs(basename):
+            basename = os.path.join(prefix, basename)
+        if 'dsv' in extensions:
+            # process dsv files recursively
+            commands += process_dsv_file(
+                basename + '.dsv', prefix, primary_extension=primary_extension,
+                additional_extension=additional_extension)
+        elif primary_extension in extensions and len(extensions) == 1:
+            # source primary-only files
+            commands += [
+                FORMAT_STR_INVOKE_SCRIPT.format_map({
+                    'prefix': prefix,
+                    'script_path': basename + '.' + primary_extension})]
+        elif additional_extension in extensions:
+            # source non-primary files
+            commands += [
+                FORMAT_STR_INVOKE_SCRIPT.format_map({
+                    'prefix': prefix,
+                    'script_path': basename + '.' + additional_extension})]
+
+    return commands
+
+
+def handle_dsv_types_except_source(type_, remainder, prefix):
+    commands = []
+    if type_ in (DSV_TYPE_SET, DSV_TYPE_SET_IF_UNSET):
+        try:
+            env_name, value = remainder.split(';', 1)
+        except ValueError:
+            raise RuntimeError(
+                "doesn't contain a semicolon separating the environment name "
+                'from the value')
+        try_prefixed_value = os.path.join(prefix, value) if value else prefix
+        if os.path.exists(try_prefixed_value):
+            value = try_prefixed_value
+        if type_ == DSV_TYPE_SET:
+            commands += _set(env_name, value)
+        elif type_ == DSV_TYPE_SET_IF_UNSET:
+            commands += _set_if_unset(env_name, value)
+        else:
+            assert False
+    elif type_ in (
+        DSV_TYPE_APPEND_NON_DUPLICATE,
+        DSV_TYPE_PREPEND_NON_DUPLICATE,
+        DSV_TYPE_PREPEND_NON_DUPLICATE_IF_EXISTS
+    ):
+        try:
+            env_name_and_values = remainder.split(';')
+        except ValueError:
+            raise RuntimeError(
+                "doesn't contain a semicolon separating the environment name "
+                'from the values')
+        env_name = env_name_and_values[0]
+        values = env_name_and_values[1:]
+        for value in values:
+            if not value:
+                value = prefix
+            elif not os.path.isabs(value):
+                value = os.path.join(prefix, value)
+            if (
+                type_ == DSV_TYPE_PREPEND_NON_DUPLICATE_IF_EXISTS and
+                not os.path.exists(value)
+            ):
+                comment = f'skip extending {env_name} with not existing ' \
+                    f'path: {value}'
+                if _include_comments():
+                    commands.append(
+                        FORMAT_STR_COMMENT_LINE.format_map({'comment': comment}))
+            elif type_ == DSV_TYPE_APPEND_NON_DUPLICATE:
+                commands += _append_unique_value(env_name, value)
+            else:
+                commands += _prepend_unique_value(env_name, value)
+    else:
+        raise RuntimeError(
+            'contains an unknown environment hook type: ' + type_)
+    return commands
+
+
+env_state = {}
+
+
+def _append_unique_value(name, value):
+    global env_state
+    if name not in env_state:
+        if os.environ.get(name):
+            env_state[name] = set(os.environ[name].split(os.pathsep))
+        else:
+            env_state[name] = set()
+    # append even if the variable has not been set yet, in case a shell script sets the
+    # same variable without the knowledge of this Python script.
+    # later _remove_ending_separators() will cleanup any unintentional leading separator
+    extend = FORMAT_STR_USE_ENV_VAR.format_map({'name': name}) + os.pathsep
+    line = FORMAT_STR_SET_ENV_VAR.format_map(
+        {'name': name, 'value': extend + value})
+    if value not in env_state[name]:
+        env_state[name].add(value)
+    else:
+        if not _include_comments():
+            return []
+        line = FORMAT_STR_COMMENT_LINE.format_map({'comment': line})
+    return [line]
+
+
+def _prepend_unique_value(name, value):
+    global env_state
+    if name not in env_state:
+        if os.environ.get(name):
+            env_state[name] = set(os.environ[name].split(os.pathsep))
+        else:
+            env_state[name] = set()
+    # prepend even if the variable has not been set yet, in case a shell script sets the
+    # same variable without the knowledge of this Python script.
+    # later _remove_ending_separators() will cleanup any unintentional trailing separator
+    extend = os.pathsep + FORMAT_STR_USE_ENV_VAR.format_map({'name': name})
+    line = FORMAT_STR_SET_ENV_VAR.format_map(
+        {'name': name, 'value': value + extend})
+    if value not in env_state[name]:
+        env_state[name].add(value)
+    else:
+        if not _include_comments():
+            return []
+        line = FORMAT_STR_COMMENT_LINE.format_map({'comment': line})
+    return [line]
+
+
+# generate commands for removing prepended underscores
+def _remove_ending_separators():
+    # do nothing if the shell extension does not implement the logic
+    if FORMAT_STR_REMOVE_TRAILING_SEPARATOR is None:
+        return []
+
+    global env_state
+    commands = []
+    for name in env_state:
+        # skip variables that already had values before this script started prepending
+        if name in os.environ:
+            continue
+        commands += [
+            FORMAT_STR_REMOVE_LEADING_SEPARATOR.format_map({'name': name}),
+            FORMAT_STR_REMOVE_TRAILING_SEPARATOR.format_map({'name': name})]
+    return commands
+
+
+def _set(name, value):
+    global env_state
+    env_state[name] = value
+    line = FORMAT_STR_SET_ENV_VAR.format_map(
+        {'name': name, 'value': value})
+    return [line]
+
+
+def _set_if_unset(name, value):
+    global env_state
+    line = FORMAT_STR_SET_ENV_VAR.format_map(
+        {'name': name, 'value': value})
+    if env_state.get(name, os.environ.get(name)):
+        line = FORMAT_STR_COMMENT_LINE.format_map({'comment': line})
+    return [line]
+
+
+if __name__ == '__main__':  # pragma: no cover
+    try:
+        rc = main()
+    except RuntimeError as e:
+        print(str(e), file=sys.stderr)
+        rc = 1
+    sys.exit(rc)
diff --git a/marshall/install/_local_setup_util_sh.py b/marshall/install/_local_setup_util_sh.py
new file mode 100644
index 0000000..35c017b
--- /dev/null
+++ b/marshall/install/_local_setup_util_sh.py
@@ -0,0 +1,404 @@
+# Copyright 2016-2019 Dirk Thomas
+# Licensed under the Apache License, Version 2.0
+
+import argparse
+from collections import OrderedDict
+import os
+from pathlib import Path
+import sys
+
+
+FORMAT_STR_COMMENT_LINE = '# {comment}'
+FORMAT_STR_SET_ENV_VAR = 'export {name}="{value}"'
+FORMAT_STR_USE_ENV_VAR = '${name}'
+FORMAT_STR_INVOKE_SCRIPT = 'COLCON_CURRENT_PREFIX="{prefix}" _colcon_prefix_sh_source_script "{script_path}"'
+FORMAT_STR_REMOVE_LEADING_SEPARATOR = 'if [ "$(echo -n ${name} | head -c 1)" = ":" ]; then export {name}=${{{name}#?}} ; fi'
+FORMAT_STR_REMOVE_TRAILING_SEPARATOR = 'if [ "$(echo -n ${name} | tail -c 1)" = ":" ]; then export {name}=${{{name}%?}} ; fi'
+
+DSV_TYPE_APPEND_NON_DUPLICATE = 'append-non-duplicate'
+DSV_TYPE_PREPEND_NON_DUPLICATE = 'prepend-non-duplicate'
+DSV_TYPE_PREPEND_NON_DUPLICATE_IF_EXISTS = 'prepend-non-duplicate-if-exists'
+DSV_TYPE_SET = 'set'
+DSV_TYPE_SET_IF_UNSET = 'set-if-unset'
+DSV_TYPE_SOURCE = 'source'
+
+
+def main(argv=sys.argv[1:]):  # noqa: D103
+    parser = argparse.ArgumentParser(
+        description='Output shell commands for the packages in topological '
+                    'order')
+    parser.add_argument(
+        'primary_extension',
+        help='The file extension of the primary shell')
+    parser.add_argument(
+        'additional_extension', nargs='?',
+        help='The additional file extension to be considered')
+    parser.add_argument(
+        '--merged-install', action='store_true',
+        help='All install prefixes are merged into a single location')
+    args = parser.parse_args(argv)
+
+    packages = get_packages(Path(__file__).parent, args.merged_install)
+
+    ordered_packages = order_packages(packages)
+    for pkg_name in ordered_packages:
+        if _include_comments():
+            print(
+                FORMAT_STR_COMMENT_LINE.format_map(
+                    {'comment': 'Package: ' + pkg_name}))
+        prefix = os.path.abspath(os.path.dirname(__file__))
+        if not args.merged_install:
+            prefix = os.path.join(prefix, pkg_name)
+        for line in get_commands(
+            pkg_name, prefix, args.primary_extension,
+            args.additional_extension
+        ):
+            print(line)
+
+    for line in _remove_ending_separators():
+        print(line)
+
+
+def get_packages(prefix_path, merged_install):
+    """
+    Find packages based on colcon-specific files created during installation.
+
+    :param Path prefix_path: The install prefix path of all packages
+    :param bool merged_install: The flag if the packages are all installed
+      directly in the prefix or if each package is installed in a subdirectory
+      named after the package
+    :returns: A mapping from the package name to the set of runtime
+      dependencies
+    :rtype: dict
+    """
+    packages = {}
+    # since importing colcon_core isn't feasible here the following constant
+    # must match colcon_core.location.get_relative_package_index_path()
+    subdirectory = 'share/colcon-core/packages'
+    if merged_install:
+        # return if workspace is empty
+        if not (prefix_path / subdirectory).is_dir():
+            return packages
+        # find all files in the subdirectory
+        for p in (prefix_path / subdirectory).iterdir():
+            if not p.is_file():
+                continue
+            if p.name.startswith('.'):
+                continue
+            add_package_runtime_dependencies(p, packages)
+    else:
+        # for each subdirectory look for the package specific file
+        for p in prefix_path.iterdir():
+            if not p.is_dir():
+                continue
+            if p.name.startswith('.'):
+                continue
+            p = p / subdirectory / p.name
+            if p.is_file():
+                add_package_runtime_dependencies(p, packages)
+
+    # remove unknown dependencies
+    pkg_names = set(packages.keys())
+    for k in packages.keys():
+        packages[k] = {d for d in packages[k] if d in pkg_names}
+
+    return packages
+
+
+def add_package_runtime_dependencies(path, packages):
+    """
+    Check the path and if it exists extract the packages runtime dependencies.
+
+    :param Path path: The resource file containing the runtime dependencies
+    :param dict packages: A mapping from package names to the sets of runtime
+      dependencies to add to
+    """
+    content = path.read_text()
+    dependencies = set(content.split(os.pathsep) if content else [])
+    packages[path.name] = dependencies
+
+
+def order_packages(packages):
+    """
+    Order packages topologically.
+
+    :param dict packages: A mapping from package name to the set of runtime
+      dependencies
+    :returns: The package names
+    :rtype: list
+    """
+    # select packages with no dependencies in alphabetical order
+    to_be_ordered = list(packages.keys())
+    ordered = []
+    while to_be_ordered:
+        pkg_names_without_deps = [
+            name for name in to_be_ordered if not packages[name]]
+        if not pkg_names_without_deps:
+            reduce_cycle_set(packages)
+            raise RuntimeError(
+                'Circular dependency between: ' + ', '.join(sorted(packages)))
+        pkg_names_without_deps.sort()
+        pkg_name = pkg_names_without_deps[0]
+        to_be_ordered.remove(pkg_name)
+        ordered.append(pkg_name)
+        # remove item from dependency lists
+        for k in list(packages.keys()):
+            if pkg_name in packages[k]:
+                packages[k].remove(pkg_name)
+    return ordered
+
+
+def reduce_cycle_set(packages):
+    """
+    Reduce the set of packages to the ones part of the circular dependency.
+
+    :param dict packages: A mapping from package name to the set of runtime
+      dependencies which is modified in place
+    """
+    last_depended = None
+    while len(packages) > 0:
+        # get all remaining dependencies
+        depended = set()
+        for pkg_name, dependencies in packages.items():
+            depended = depended.union(dependencies)
+        # remove all packages which are not dependent on
+        for name in list(packages.keys()):
+            if name not in depended:
+                del packages[name]
+        if last_depended:
+            # if remaining packages haven't changed return them
+            if last_depended == depended:
+                return packages.keys()
+        # otherwise reduce again
+        last_depended = depended
+
+
+def _include_comments():
+    # skipping comment lines when COLCON_TRACE is not set speeds up the
+    # processing especially on Windows
+    return bool(os.environ.get('COLCON_TRACE'))
+
+
+def get_commands(pkg_name, prefix, primary_extension, additional_extension):
+    commands = []
+    package_dsv_path = os.path.join(prefix, 'share', pkg_name, 'package.dsv')
+    if os.path.exists(package_dsv_path):
+        commands += process_dsv_file(
+            package_dsv_path, prefix, primary_extension, additional_extension)
+    return commands
+
+
+def process_dsv_file(
+    dsv_path, prefix, primary_extension=None, additional_extension=None
+):
+    commands = []
+    if _include_comments():
+        commands.append(FORMAT_STR_COMMENT_LINE.format_map({'comment': dsv_path}))
+    with open(dsv_path, 'r') as h:
+        content = h.read()
+    lines = content.splitlines()
+
+    basenames = OrderedDict()
+    for i, line in enumerate(lines):
+        # skip over empty or whitespace-only lines
+        if not line.strip():
+            continue
+        try:
+            type_, remainder = line.split(';', 1)
+        except ValueError:
+            raise RuntimeError(
+                "Line %d in '%s' doesn't contain a semicolon separating the "
+                'type from the arguments' % (i + 1, dsv_path))
+        if type_ != DSV_TYPE_SOURCE:
+            # handle non-source lines
+            try:
+                commands += handle_dsv_types_except_source(
+                    type_, remainder, prefix)
+            except RuntimeError as e:
+                raise RuntimeError(
+                    "Line %d in '%s' %s" % (i + 1, dsv_path, e)) from e
+        else:
+            # group remaining source lines by basename
+            path_without_ext, ext = os.path.splitext(remainder)
+            if path_without_ext not in basenames:
+                basenames[path_without_ext] = set()
+            assert ext.startswith('.')
+            ext = ext[1:]
+            if ext in (primary_extension, additional_extension):
+                basenames[path_without_ext].add(ext)
+
+    # add the dsv extension to each basename if the file exists
+    for basename, extensions in basenames.items():
+        if not os.path.isabs(basename):
+            basename = os.path.join(prefix, basename)
+        if os.path.exists(basename + '.dsv'):
+            extensions.add('dsv')
+
+    for basename, extensions in basenames.items():
+        if not os.path.isabs(basename):
+            basename = os.path.join(prefix, basename)
+        if 'dsv' in extensions:
+            # process dsv files recursively
+            commands += process_dsv_file(
+                basename + '.dsv', prefix, primary_extension=primary_extension,
+                additional_extension=additional_extension)
+        elif primary_extension in extensions and len(extensions) == 1:
+            # source primary-only files
+            commands += [
+                FORMAT_STR_INVOKE_SCRIPT.format_map({
+                    'prefix': prefix,
+                    'script_path': basename + '.' + primary_extension})]
+        elif additional_extension in extensions:
+            # source non-primary files
+            commands += [
+                FORMAT_STR_INVOKE_SCRIPT.format_map({
+                    'prefix': prefix,
+                    'script_path': basename + '.' + additional_extension})]
+
+    return commands
+
+
+def handle_dsv_types_except_source(type_, remainder, prefix):
+    commands = []
+    if type_ in (DSV_TYPE_SET, DSV_TYPE_SET_IF_UNSET):
+        try:
+            env_name, value = remainder.split(';', 1)
+        except ValueError:
+            raise RuntimeError(
+                "doesn't contain a semicolon separating the environment name "
+                'from the value')
+        try_prefixed_value = os.path.join(prefix, value) if value else prefix
+        if os.path.exists(try_prefixed_value):
+            value = try_prefixed_value
+        if type_ == DSV_TYPE_SET:
+            commands += _set(env_name, value)
+        elif type_ == DSV_TYPE_SET_IF_UNSET:
+            commands += _set_if_unset(env_name, value)
+        else:
+            assert False
+    elif type_ in (
+        DSV_TYPE_APPEND_NON_DUPLICATE,
+        DSV_TYPE_PREPEND_NON_DUPLICATE,
+        DSV_TYPE_PREPEND_NON_DUPLICATE_IF_EXISTS
+    ):
+        try:
+            env_name_and_values = remainder.split(';')
+        except ValueError:
+            raise RuntimeError(
+                "doesn't contain a semicolon separating the environment name "
+                'from the values')
+        env_name = env_name_and_values[0]
+        values = env_name_and_values[1:]
+        for value in values:
+            if not value:
+                value = prefix
+            elif not os.path.isabs(value):
+                value = os.path.join(prefix, value)
+            if (
+                type_ == DSV_TYPE_PREPEND_NON_DUPLICATE_IF_EXISTS and
+                not os.path.exists(value)
+            ):
+                comment = f'skip extending {env_name} with not existing ' \
+                    f'path: {value}'
+                if _include_comments():
+                    commands.append(
+                        FORMAT_STR_COMMENT_LINE.format_map({'comment': comment}))
+            elif type_ == DSV_TYPE_APPEND_NON_DUPLICATE:
+                commands += _append_unique_value(env_name, value)
+            else:
+                commands += _prepend_unique_value(env_name, value)
+    else:
+        raise RuntimeError(
+            'contains an unknown environment hook type: ' + type_)
+    return commands
+
+
+env_state = {}
+
+
+def _append_unique_value(name, value):
+    global env_state
+    if name not in env_state:
+        if os.environ.get(name):
+            env_state[name] = set(os.environ[name].split(os.pathsep))
+        else:
+            env_state[name] = set()
+    # append even if the variable has not been set yet, in case a shell script sets the
+    # same variable without the knowledge of this Python script.
+    # later _remove_ending_separators() will cleanup any unintentional leading separator
+    extend = FORMAT_STR_USE_ENV_VAR.format_map({'name': name}) + os.pathsep
+    line = FORMAT_STR_SET_ENV_VAR.format_map(
+        {'name': name, 'value': extend + value})
+    if value not in env_state[name]:
+        env_state[name].add(value)
+    else:
+        if not _include_comments():
+            return []
+        line = FORMAT_STR_COMMENT_LINE.format_map({'comment': line})
+    return [line]
+
+
+def _prepend_unique_value(name, value):
+    global env_state
+    if name not in env_state:
+        if os.environ.get(name):
+            env_state[name] = set(os.environ[name].split(os.pathsep))
+        else:
+            env_state[name] = set()
+    # prepend even if the variable has not been set yet, in case a shell script sets the
+    # same variable without the knowledge of this Python script.
+    # later _remove_ending_separators() will cleanup any unintentional trailing separator
+    extend = os.pathsep + FORMAT_STR_USE_ENV_VAR.format_map({'name': name})
+    line = FORMAT_STR_SET_ENV_VAR.format_map(
+        {'name': name, 'value': value + extend})
+    if value not in env_state[name]:
+        env_state[name].add(value)
+    else:
+        if not _include_comments():
+            return []
+        line = FORMAT_STR_COMMENT_LINE.format_map({'comment': line})
+    return [line]
+
+
+# generate commands for removing prepended underscores
+def _remove_ending_separators():
+    # do nothing if the shell extension does not implement the logic
+    if FORMAT_STR_REMOVE_TRAILING_SEPARATOR is None:
+        return []
+
+    global env_state
+    commands = []
+    for name in env_state:
+        # skip variables that already had values before this script started prepending
+        if name in os.environ:
+            continue
+        commands += [
+            FORMAT_STR_REMOVE_LEADING_SEPARATOR.format_map({'name': name}),
+            FORMAT_STR_REMOVE_TRAILING_SEPARATOR.format_map({'name': name})]
+    return commands
+
+
+def _set(name, value):
+    global env_state
+    env_state[name] = value
+    line = FORMAT_STR_SET_ENV_VAR.format_map(
+        {'name': name, 'value': value})
+    return [line]
+
+
+def _set_if_unset(name, value):
+    global env_state
+    line = FORMAT_STR_SET_ENV_VAR.format_map(
+        {'name': name, 'value': value})
+    if env_state.get(name, os.environ.get(name)):
+        line = FORMAT_STR_COMMENT_LINE.format_map({'comment': line})
+    return [line]
+
+
+if __name__ == '__main__':  # pragma: no cover
+    try:
+        rc = main()
+    except RuntimeError as e:
+        print(str(e), file=sys.stderr)
+        rc = 1
+    sys.exit(rc)
diff --git a/marshall/install/local_setup.bash b/marshall/install/local_setup.bash
new file mode 100644
index 0000000..efd5f8c
--- /dev/null
+++ b/marshall/install/local_setup.bash
@@ -0,0 +1,107 @@
+# generated from colcon_bash/shell/template/prefix.bash.em
+
+# This script extends the environment with all packages contained in this
+# prefix path.
+
+# a bash script is able to determine its own path if necessary
+if [ -z "$COLCON_CURRENT_PREFIX" ]; then
+  _colcon_prefix_bash_COLCON_CURRENT_PREFIX="$(builtin cd "`dirname "${BASH_SOURCE[0]}"`" > /dev/null && pwd)"
+else
+  _colcon_prefix_bash_COLCON_CURRENT_PREFIX="$COLCON_CURRENT_PREFIX"
+fi
+
+# function to prepend a value to a variable
+# which uses colons as separators
+# duplicates as well as trailing separators are avoided
+# first argument: the name of the result variable
+# second argument: the value to be prepended
+_colcon_prefix_bash_prepend_unique_value() {
+  # arguments
+  _listname="$1"
+  _value="$2"
+
+  # get values from variable
+  eval _values=\"\$$_listname\"
+  # backup the field separator
+  _colcon_prefix_bash_prepend_unique_value_IFS="$IFS"
+  IFS=":"
+  # start with the new value
+  _all_values="$_value"
+  # iterate over existing values in the variable
+  for _item in $_values; do
+    # ignore empty strings
+    if [ -z "$_item" ]; then
+      continue
+    fi
+    # ignore duplicates of _value
+    if [ "$_item" = "$_value" ]; then
+      continue
+    fi
+    # keep non-duplicate values
+    _all_values="$_all_values:$_item"
+  done
+  unset _item
+  # restore the field separator
+  IFS="$_colcon_prefix_bash_prepend_unique_value_IFS"
+  unset _colcon_prefix_bash_prepend_unique_value_IFS
+  # export the updated variable
+  eval export $_listname=\"$_all_values\"
+  unset _all_values
+  unset _values
+
+  unset _value
+  unset _listname
+}
+
+# add this prefix to the COLCON_PREFIX_PATH
+_colcon_prefix_bash_prepend_unique_value COLCON_PREFIX_PATH "$_colcon_prefix_bash_COLCON_CURRENT_PREFIX"
+unset _colcon_prefix_bash_prepend_unique_value
+
+# check environment variable for custom Python executable
+if [ -n "$COLCON_PYTHON_EXECUTABLE" ]; then
+  if [ ! -f "$COLCON_PYTHON_EXECUTABLE" ]; then
+    echo "error: COLCON_PYTHON_EXECUTABLE '$COLCON_PYTHON_EXECUTABLE' doesn't exist"
+    return 1
+  fi
+  _colcon_python_executable="$COLCON_PYTHON_EXECUTABLE"
+else
+  # try the Python executable known at configure time
+  _colcon_python_executable="/usr/bin/python3"
+  # if it doesn't exist try a fall back
+  if [ ! -f "$_colcon_python_executable" ]; then
+    if ! /usr/bin/env python3 --version > /dev/null 2> /dev/null; then
+      echo "error: unable to find python3 executable"
+      return 1
+    fi
+    _colcon_python_executable=`/usr/bin/env python3 -c "import sys; print(sys.executable)"`
+  fi
+fi
+
+# function to source another script with conditional trace output
+# first argument: the path of the script
+_colcon_prefix_sh_source_script() {
+  if [ -f "$1" ]; then
+    if [ -n "$COLCON_TRACE" ]; then
+      echo ". \"$1\""
+    fi
+    . "$1"
+  else
+    echo "not found: \"$1\"" 1>&2
+  fi
+}
+
+# get all commands in topological order
+_colcon_ordered_commands="$($_colcon_python_executable "$_colcon_prefix_bash_COLCON_CURRENT_PREFIX/_local_setup_util_sh.py" sh bash)"
+unset _colcon_python_executable
+if [ -n "$COLCON_TRACE" ]; then
+  echo "Execute generated script:"
+  echo "<<<"
+  echo "${_colcon_ordered_commands}"
+  echo ">>>"
+fi
+eval "${_colcon_ordered_commands}"
+unset _colcon_ordered_commands
+
+unset _colcon_prefix_sh_source_script
+
+unset _colcon_prefix_bash_COLCON_CURRENT_PREFIX
diff --git a/marshall/install/local_setup.ps1 b/marshall/install/local_setup.ps1
new file mode 100644
index 0000000..6f68c8d
--- /dev/null
+++ b/marshall/install/local_setup.ps1
@@ -0,0 +1,55 @@
+# generated from colcon_powershell/shell/template/prefix.ps1.em
+
+# This script extends the environment with all packages contained in this
+# prefix path.
+
+# check environment variable for custom Python executable
+if ($env:COLCON_PYTHON_EXECUTABLE) {
+  if (!(Test-Path "$env:COLCON_PYTHON_EXECUTABLE" -PathType Leaf)) {
+    echo "error: COLCON_PYTHON_EXECUTABLE '$env:COLCON_PYTHON_EXECUTABLE' doesn't exist"
+    exit 1
+  }
+  $_colcon_python_executable="$env:COLCON_PYTHON_EXECUTABLE"
+} else {
+  # use the Python executable known at configure time
+  $_colcon_python_executable="/usr/bin/python3"
+  # if it doesn't exist try a fall back
+  if (!(Test-Path "$_colcon_python_executable" -PathType Leaf)) {
+    if (!(Get-Command "python3" -ErrorAction SilentlyContinue)) {
+      echo "error: unable to find python3 executable"
+      exit 1
+    }
+    $_colcon_python_executable="python3"
+  }
+}
+
+# function to source another script with conditional trace output
+# first argument: the path of the script
+function _colcon_prefix_powershell_source_script {
+  param (
+    $_colcon_prefix_powershell_source_script_param
+  )
+  # source script with conditional trace output
+  if (Test-Path $_colcon_prefix_powershell_source_script_param) {
+    if ($env:COLCON_TRACE) {
+      echo ". '$_colcon_prefix_powershell_source_script_param'"
+    }
+    . "$_colcon_prefix_powershell_source_script_param"
+  } else {
+    Write-Error "not found: '$_colcon_prefix_powershell_source_script_param'"
+  }
+}
+
+# get all commands in topological order
+$_colcon_ordered_commands = & "$_colcon_python_executable" "$(Split-Path $PSCommandPath -Parent)/_local_setup_util_ps1.py" ps1
+
+# execute all commands in topological order
+if ($env:COLCON_TRACE) {
+  echo "Execute generated script:"
+  echo "<<<"
+  $_colcon_ordered_commands.Split([Environment]::NewLine, [StringSplitOptions]::RemoveEmptyEntries) | Write-Output
+  echo ">>>"
+}
+if ($_colcon_ordered_commands) {
+  $_colcon_ordered_commands.Split([Environment]::NewLine, [StringSplitOptions]::RemoveEmptyEntries) | Invoke-Expression
+}
diff --git a/marshall/install/local_setup.sh b/marshall/install/local_setup.sh
new file mode 100644
index 0000000..7be8813
--- /dev/null
+++ b/marshall/install/local_setup.sh
@@ -0,0 +1,137 @@
+# generated from colcon_core/shell/template/prefix.sh.em
+
+# This script extends the environment with all packages contained in this
+# prefix path.
+
+# since a plain shell script can't determine its own path when being sourced
+# either use the provided COLCON_CURRENT_PREFIX
+# or fall back to the build time prefix (if it exists)
+_colcon_prefix_sh_COLCON_CURRENT_PREFIX="/home/grimmlins/Documents/GitHub/treefitting/marshall/install"
+if [ -z "$COLCON_CURRENT_PREFIX" ]; then
+  if [ ! -d "$_colcon_prefix_sh_COLCON_CURRENT_PREFIX" ]; then
+    echo "The build time path \"$_colcon_prefix_sh_COLCON_CURRENT_PREFIX\" doesn't exist. Either source a script for a different shell or set the environment variable \"COLCON_CURRENT_PREFIX\" explicitly." 1>&2
+    unset _colcon_prefix_sh_COLCON_CURRENT_PREFIX
+    return 1
+  fi
+else
+  _colcon_prefix_sh_COLCON_CURRENT_PREFIX="$COLCON_CURRENT_PREFIX"
+fi
+
+# function to prepend a value to a variable
+# which uses colons as separators
+# duplicates as well as trailing separators are avoided
+# first argument: the name of the result variable
+# second argument: the value to be prepended
+_colcon_prefix_sh_prepend_unique_value() {
+  # arguments
+  _listname="$1"
+  _value="$2"
+
+  # get values from variable
+  eval _values=\"\$$_listname\"
+  # backup the field separator
+  _colcon_prefix_sh_prepend_unique_value_IFS="$IFS"
+  IFS=":"
+  # start with the new value
+  _all_values="$_value"
+  _contained_value=""
+  # iterate over existing values in the variable
+  for _item in $_values; do
+    # ignore empty strings
+    if [ -z "$_item" ]; then
+      continue
+    fi
+    # ignore duplicates of _value
+    if [ "$_item" = "$_value" ]; then
+      _contained_value=1
+      continue
+    fi
+    # keep non-duplicate values
+    _all_values="$_all_values:$_item"
+  done
+  unset _item
+  if [ -z "$_contained_value" ]; then
+    if [ -n "$COLCON_TRACE" ]; then
+      if [ "$_all_values" = "$_value" ]; then
+        echo "export $_listname=$_value"
+      else
+        echo "export $_listname=$_value:\$$_listname"
+      fi
+    fi
+  fi
+  unset _contained_value
+  # restore the field separator
+  IFS="$_colcon_prefix_sh_prepend_unique_value_IFS"
+  unset _colcon_prefix_sh_prepend_unique_value_IFS
+  # export the updated variable
+  eval export $_listname=\"$_all_values\"
+  unset _all_values
+  unset _values
+
+  unset _value
+  unset _listname
+}
+
+# add this prefix to the COLCON_PREFIX_PATH
+_colcon_prefix_sh_prepend_unique_value COLCON_PREFIX_PATH "$_colcon_prefix_sh_COLCON_CURRENT_PREFIX"
+unset _colcon_prefix_sh_prepend_unique_value
+
+# check environment variable for custom Python executable
+if [ -n "$COLCON_PYTHON_EXECUTABLE" ]; then
+  if [ ! -f "$COLCON_PYTHON_EXECUTABLE" ]; then
+    echo "error: COLCON_PYTHON_EXECUTABLE '$COLCON_PYTHON_EXECUTABLE' doesn't exist"
+    return 1
+  fi
+  _colcon_python_executable="$COLCON_PYTHON_EXECUTABLE"
+else
+  # try the Python executable known at configure time
+  _colcon_python_executable="/usr/bin/python3"
+  # if it doesn't exist try a fall back
+  if [ ! -f "$_colcon_python_executable" ]; then
+    if ! /usr/bin/env python3 --version > /dev/null 2> /dev/null; then
+      echo "error: unable to find python3 executable"
+      return 1
+    fi
+    _colcon_python_executable=`/usr/bin/env python3 -c "import sys; print(sys.executable)"`
+  fi
+fi
+
+# function to source another script with conditional trace output
+# first argument: the path of the script
+_colcon_prefix_sh_source_script() {
+  if [ -f "$1" ]; then
+    if [ -n "$COLCON_TRACE" ]; then
+      echo "# . \"$1\""
+    fi
+    . "$1"
+  else
+    echo "not found: \"$1\"" 1>&2
+  fi
+}
+
+# get all commands in topological order
+_colcon_ordered_commands="$($_colcon_python_executable "$_colcon_prefix_sh_COLCON_CURRENT_PREFIX/_local_setup_util_sh.py" sh)"
+unset _colcon_python_executable
+if [ -n "$COLCON_TRACE" ]; then
+  echo "_colcon_prefix_sh_source_script() {
+    if [ -f \"\$1\" ]; then
+      if [ -n \"\$COLCON_TRACE\" ]; then
+        echo \"# . \\\"\$1\\\"\"
+      fi
+      . \"\$1\"
+    else
+      echo \"not found: \\\"\$1\\\"\" 1>&2
+    fi
+  }"
+  echo "# Execute generated script:"
+  echo "# <<<"
+  echo "${_colcon_ordered_commands}"
+  echo "# >>>"
+  echo "unset _colcon_prefix_sh_source_script"
+fi
+eval "${_colcon_ordered_commands}"
+unset _colcon_ordered_commands
+
+unset _colcon_prefix_sh_source_script
+
+unset _colcon_prefix_sh_COLCON_CURRENT_PREFIX
diff --git a/marshall/install/local_setup.zsh b/marshall/install/local_setup.zsh
new file mode 100644
index 0000000..f7a8d90
--- /dev/null
+++ b/marshall/install/local_setup.zsh
@@ -0,0 +1,120 @@
+# generated from colcon_zsh/shell/template/prefix.zsh.em
+
+# This script extends the environment with all packages contained in this
+# prefix path.
+
+# a zsh script is able to determine its own path if necessary
+if [ -z "$COLCON_CURRENT_PREFIX" ]; then
+  _colcon_prefix_zsh_COLCON_CURRENT_PREFIX="$(builtin cd -q "`dirname "${(%):-%N}"`" > /dev/null && pwd)"
+else
+  _colcon_prefix_zsh_COLCON_CURRENT_PREFIX="$COLCON_CURRENT_PREFIX"
+fi
+
+# function to convert array-like strings into arrays
+# to workaround SH_WORD_SPLIT not being set
+_colcon_prefix_zsh_convert_to_array() {
+  local _listname=$1
+  local _dollar="$"
+  local _split="{="
+  local _to_array="(\"$_dollar$_split$_listname}\")"
+  eval $_listname=$_to_array
+}
+
+# function to prepend a value to a variable
+# which uses colons as separators
+# duplicates as well as trailing separators are avoided
+# first argument: the name of the result variable
+# second argument: the value to be prepended
+_colcon_prefix_zsh_prepend_unique_value() {
+  # arguments
+  _listname="$1"
+  _value="$2"
+
+  # get values from variable
+  eval _values=\"\$$_listname\"
+  # backup the field separator
+  _colcon_prefix_zsh_prepend_unique_value_IFS="$IFS"
+  IFS=":"
+  # start with the new value
+  _all_values="$_value"
+  # workaround SH_WORD_SPLIT not being set
+  _colcon_prefix_zsh_convert_to_array _values
+  # iterate over existing values in the variable
+  for _item in $_values; do
+    # ignore empty strings
+    if [ -z "$_item" ]; then
+      continue
+    fi
+    # ignore duplicates of _value
+    if [ "$_item" = "$_value" ]; then
+      continue
+    fi
+    # keep non-duplicate values
+    _all_values="$_all_values:$_item"
+  done
+  unset _item
+  # restore the field separator
+  IFS="$_colcon_prefix_zsh_prepend_unique_value_IFS"
+  unset _colcon_prefix_zsh_prepend_unique_value_IFS
+  # export the updated variable
+  eval export $_listname=\"$_all_values\"
+  unset _all_values
+  unset _values
+
+  unset _value
+  unset _listname
+}
+
+# add this prefix to the COLCON_PREFIX_PATH
+_colcon_prefix_zsh_prepend_unique_value COLCON_PREFIX_PATH "$_colcon_prefix_zsh_COLCON_CURRENT_PREFIX"
+unset _colcon_prefix_zsh_prepend_unique_value
+unset _colcon_prefix_zsh_convert_to_array
+
+# check environment variable for custom Python executable
+if [ -n "$COLCON_PYTHON_EXECUTABLE" ]; then
+  if [ ! -f "$COLCON_PYTHON_EXECUTABLE" ]; then
+    echo "error: COLCON_PYTHON_EXECUTABLE '$COLCON_PYTHON_EXECUTABLE' doesn't exist"
+    return 1
+  fi
+  _colcon_python_executable="$COLCON_PYTHON_EXECUTABLE"
+else
+  # try the Python executable known at configure time
+  _colcon_python_executable="/usr/bin/python3"
+  # if it doesn't exist try a fall back
+  if [ ! -f "$_colcon_python_executable" ]; then
+    if ! /usr/bin/env python3 --version > /dev/null 2> /dev/null; then
+      echo "error: unable to find python3 executable"
+      return 1
+    fi
+    _colcon_python_executable=`/usr/bin/env python3 -c "import sys; print(sys.executable)"`
+  fi
+fi
+
+# function to source another script with conditional trace output
+# first argument: the path of the script
+_colcon_prefix_sh_source_script() {
+  if [ -f "$1" ]; then
+    if [ -n "$COLCON_TRACE" ]; then
+      echo ". \"$1\""
+    fi
+    . "$1"
+  else
+    echo "not found: \"$1\"" 1>&2
+  fi
+}
+
+# get all commands in topological order
+_colcon_ordered_commands="$($_colcon_python_executable "$_colcon_prefix_zsh_COLCON_CURRENT_PREFIX/_local_setup_util_sh.py" sh zsh)"
+unset _colcon_python_executable
+if [ -n "$COLCON_TRACE" ]; then
+  echo "Execute generated script:"
+  echo "<<<"
+  echo "${_colcon_ordered_commands}"
+  echo ">>>"
+fi
+eval "${_colcon_ordered_commands}"
+unset _colcon_ordered_commands
+
+unset _colcon_prefix_sh_source_script
+
+unset _colcon_prefix_zsh_COLCON_CURRENT_PREFIX
diff --git a/marshall/install/setup.bash b/marshall/install/setup.bash
new file mode 100644
index 0000000..4c55244
--- /dev/null
+++ b/marshall/install/setup.bash
@@ -0,0 +1,31 @@
+# generated from colcon_bash/shell/template/prefix_chain.bash.em
+
+# This script extends the environment with the environment of other prefix
+# paths which were sourced when this file was generated as well as all packages
+# contained in this prefix path.
+
+# function to source another script with conditional trace output
+# first argument: the path of the script
+_colcon_prefix_chain_bash_source_script() {
+  if [ -f "$1" ]; then
+    if [ -n "$COLCON_TRACE" ]; then
+      echo ". \"$1\""
+    fi
+    . "$1"
+  else
+    echo "not found: \"$1\"" 1>&2
+  fi
+}
+
+# source chained prefixes
+# setting COLCON_CURRENT_PREFIX avoids determining the prefix in the sourced script
+COLCON_CURRENT_PREFIX="/opt/ros/humble"
+_colcon_prefix_chain_bash_source_script "$COLCON_CURRENT_PREFIX/local_setup.bash"
+
+# source this prefix
+# setting COLCON_CURRENT_PREFIX avoids determining the prefix in the sourced script
+COLCON_CURRENT_PREFIX="$(builtin cd "`dirname "${BASH_SOURCE[0]}"`" > /dev/null && pwd)"
+_colcon_prefix_chain_bash_source_script "$COLCON_CURRENT_PREFIX/local_setup.bash"
+
+unset COLCON_CURRENT_PREFIX
+unset _colcon_prefix_chain_bash_source_script
diff --git a/marshall/install/setup.ps1 b/marshall/install/setup.ps1
new file mode 100644
index 0000000..558e9b9
--- /dev/null
+++ b/marshall/install/setup.ps1
@@ -0,0 +1,29 @@
+# generated from colcon_powershell/shell/template/prefix_chain.ps1.em
+
+# This script extends the environment with the environment of other prefix
+# paths which were sourced when this file was generated as well as all packages
+# contained in this prefix path.
+
+# function to source another script with conditional trace output
+# first argument: the path of the script
+function _colcon_prefix_chain_powershell_source_script {
+  param (
+    $_colcon_prefix_chain_powershell_source_script_param
+  )
+  # source script with conditional trace output
+  if (Test-Path $_colcon_prefix_chain_powershell_source_script_param) {
+    if ($env:COLCON_TRACE) {
+      echo ". '$_colcon_prefix_chain_powershell_source_script_param'"
+    }
+    . "$_colcon_prefix_chain_powershell_source_script_param"
+  } else {
+    Write-Error "not found: '$_colcon_prefix_chain_powershell_source_script_param'"
+  }
+}
+
+# source chained prefixes
+_colcon_prefix_chain_powershell_source_script "/opt/ros/humble\local_setup.ps1"
+
+# source this prefix
+$env:COLCON_CURRENT_PREFIX=(Split-Path $PSCommandPath -Parent)
+_colcon_prefix_chain_powershell_source_script "$env:COLCON_CURRENT_PREFIX\local_setup.ps1"
diff --git a/marshall/install/setup.sh b/marshall/install/setup.sh
new file mode 100644
index 0000000..7bf631b
--- /dev/null
+++ b/marshall/install/setup.sh
@@ -0,0 +1,45 @@
+# generated from colcon_core/shell/template/prefix_chain.sh.em
+
+# This script extends the environment with the environment of other prefix
+# paths which were sourced when this file was generated as well as all packages
+# contained in this prefix path.
+
+# since a plain shell script can't determine its own path when being sourced
+# either use the provided COLCON_CURRENT_PREFIX
+# or fall back to the build time prefix (if it exists)
+_colcon_prefix_chain_sh_COLCON_CURRENT_PREFIX=/home/grimmlins/Documents/GitHub/treefitting/marshall/install
+if [ ! -z "$COLCON_CURRENT_PREFIX" ]; then
+  _colcon_prefix_chain_sh_COLCON_CURRENT_PREFIX="$COLCON_CURRENT_PREFIX"
+elif [ ! -d "$_colcon_prefix_chain_sh_COLCON_CURRENT_PREFIX" ]; then
+  echo "The build time path \"$_colcon_prefix_chain_sh_COLCON_CURRENT_PREFIX\" doesn't exist. Either source a script for a different shell or set the environment variable \"COLCON_CURRENT_PREFIX\" explicitly." 1>&2
+  unset _colcon_prefix_chain_sh_COLCON_CURRENT_PREFIX
+  return 1
+fi
+
+# function to source another script with conditional trace output
+# first argument: the path of the script
+_colcon_prefix_chain_sh_source_script() {
+  if [ -f "$1" ]; then
+    if [ -n "$COLCON_TRACE" ]; then
+      echo "# . \"$1\""
+    fi
+    . "$1"
+  else
+    echo "not found: \"$1\"" 1>&2
+  fi
+}
+
+# source chained prefixes
+# setting COLCON_CURRENT_PREFIX avoids relying on the build time prefix of the sourced script
+COLCON_CURRENT_PREFIX="/opt/ros/humble"
+_colcon_prefix_chain_sh_source_script "$COLCON_CURRENT_PREFIX/local_setup.sh"
+
+
+# source this prefix
+# setting COLCON_CURRENT_PREFIX avoids relying on the build time prefix of the sourced script
+COLCON_CURRENT_PREFIX="$_colcon_prefix_chain_sh_COLCON_CURRENT_PREFIX"
+_colcon_prefix_chain_sh_source_script "$COLCON_CURRENT_PREFIX/local_setup.sh"
+
+unset _colcon_prefix_chain_sh_COLCON_CURRENT_PREFIX
+unset _colcon_prefix_chain_sh_source_script
+unset COLCON_CURRENT_PREFIX
diff --git a/marshall/install/setup.zsh b/marshall/install/setup.zsh
new file mode 100644
index 0000000..990d171
--- /dev/null
+++ b/marshall/install/setup.zsh
@@ -0,0 +1,31 @@
+# generated from colcon_zsh/shell/template/prefix_chain.zsh.em
+
+# This script extends the environment with the environment of other prefix
+# paths which were sourced when this file was generated as well as all packages
+# contained in this prefix path.
+
+# function to source another script with conditional trace output
+# first argument: the path of the script
+_colcon_prefix_chain_zsh_source_script() {
+  if [ -f "$1" ]; then
+    if [ -n "$COLCON_TRACE" ]; then
+      echo ". \"$1\""
+    fi
+    . "$1"
+  else
+    echo "not found: \"$1\"" 1>&2
+  fi
+}
+
+# source chained prefixes
+# setting COLCON_CURRENT_PREFIX avoids determining the prefix in the sourced script
+COLCON_CURRENT_PREFIX="/opt/ros/humble"
+_colcon_prefix_chain_zsh_source_script "$COLCON_CURRENT_PREFIX/local_setup.zsh"
+
+# source this prefix
+# setting COLCON_CURRENT_PREFIX avoids determining the prefix in the sourced script
+COLCON_CURRENT_PREFIX="$(builtin cd -q "`dirname "${(%):-%N}"`" > /dev/null && pwd)"
+_colcon_prefix_chain_zsh_source_script "$COLCON_CURRENT_PREFIX/local_setup.zsh"
+
+unset COLCON_CURRENT_PREFIX
+unset _colcon_prefix_chain_zsh_source_script
diff --git a/marshall/leader_mask.png b/marshall/leader_mask.png
new file mode 100644
index 0000000..39000bb
Binary files /dev/null and b/marshall/leader_mask.png differ
diff --git a/marshall/log/COLCON_IGNORE b/marshall/log/COLCON_IGNORE
new file mode 100644
index 0000000..e69de29
diff --git a/marshall/log/build_2023-09-02_12-15-53/events.log b/marshall/log/build_2023-09-02_12-15-53/events.log
new file mode 100644
index 0000000..a5b1e71
--- /dev/null
+++ b/marshall/log/build_2023-09-02_12-15-53/events.log
@@ -0,0 +1,2 @@
+[0.000000] (-) TimerEvent: {}
+[0.000517] (-) EventReactorShutdown: {}
diff --git a/marshall/log/build_2023-09-02_12-15-53/logger_all.log b/marshall/log/build_2023-09-02_12-15-53/logger_all.log
new file mode 100644
index 0000000..c365ecd
--- /dev/null
+++ b/marshall/log/build_2023-09-02_12-15-53/logger_all.log
@@ -0,0 +1,90 @@
+[0.314s] DEBUG:colcon:Command line arguments: ['/usr/bin/colcon', 'build']
+[0.314s] DEBUG:colcon:Parsed command line arguments: Namespace(log_base=None, log_level=None, verb_name='build', build_base='build', install_base='install', merge_install=False, symlink_install=False, test_result_base=None, continue_on_error=False, executor='parallel', parallel_workers=16, event_handlers=None, ignore_user_meta=False, metas=['./colcon.meta'], base_paths=['.'], packages_ignore=None, packages_ignore_regex=None, paths=None, packages_up_to=None, packages_up_to_regex=None, packages_above=None, packages_above_and_dependencies=None, packages_above_depth=None, packages_select_by_dep=None, packages_skip_by_dep=None, packages_skip_up_to=None, packages_select_build_failed=False, packages_skip_build_finished=False, packages_select_test_failures=False, packages_skip_test_passed=False, packages_select=None, packages_skip=None, packages_select_regex=None, packages_skip_regex=None, packages_start=None, packages_end=None, allow_overriding=[], cmake_args=None, cmake_target=None, cmake_target_skip_unavailable=False, cmake_clean_cache=False, cmake_clean_first=False, cmake_force_configure=False, ament_cmake_args=None, catkin_cmake_args=None, catkin_skip_building_tests=False, verb_parser=<colcon_defaults.argument_parser.defaults.DefaultArgumentsDecorator object at 0x7fba27effa30>, verb_extension=<colcon_core.verb.build.BuildVerb object at 0x7fba28688b20>, main=<bound method BuildVerb.main of <colcon_core.verb.build.BuildVerb object at 0x7fba28688b20>>)
+[0.343s] Level 1:colcon.colcon_core.package_discovery:discover_packages(colcon_meta) check parameters
+[0.343s] Level 1:colcon.colcon_core.package_discovery:discover_packages(recursive) check parameters
+[0.343s] Level 1:colcon.colcon_core.package_discovery:discover_packages(ignore) check parameters
+[0.343s] Level 1:colcon.colcon_core.package_discovery:discover_packages(path) check parameters
+[0.343s] Level 1:colcon.colcon_core.package_discovery:discover_packages(colcon_meta) discover
+[0.343s] Level 1:colcon.colcon_core.package_discovery:discover_packages(recursive) discover
+[0.343s] INFO:colcon.colcon_core.package_discovery:Crawling recursively for packages in '/home/grimmlins/Documents/GitHub/treefitting/marshall'
+[0.343s] Level 1:colcon.colcon_core.package_identification:_identify(.) by extensions ['ignore', 'ignore_ament_install']
+[0.343s] Level 1:colcon.colcon_core.package_identification:_identify(.) by extension 'ignore'
+[0.343s] Level 1:colcon.colcon_core.package_identification:_identify(.) by extension 'ignore_ament_install'
+[0.343s] Level 1:colcon.colcon_core.package_identification:_identify(.) by extensions ['colcon_pkg']
+[0.344s] Level 1:colcon.colcon_core.package_identification:_identify(.) by extension 'colcon_pkg'
+[0.344s] Level 1:colcon.colcon_core.package_identification:_identify(.) by extensions ['colcon_meta']
+[0.344s] Level 1:colcon.colcon_core.package_identification:_identify(.) by extension 'colcon_meta'
+[0.344s] Level 1:colcon.colcon_core.package_identification:_identify(.) by extensions ['ros']
+[0.344s] Level 1:colcon.colcon_core.package_identification:_identify(.) by extension 'ros'
+[0.354s] Level 1:colcon.colcon_core.package_identification:_identify(.) by extensions ['cmake', 'python']
+[0.354s] Level 1:colcon.colcon_core.package_identification:_identify(.) by extension 'cmake'
+[0.354s] Level 1:colcon.colcon_core.package_identification:_identify(.) by extension 'python'
+[0.354s] Level 1:colcon.colcon_core.package_identification:_identify(.) by extensions ['python_setup_py']
+[0.354s] Level 1:colcon.colcon_core.package_identification:_identify(.) by extension 'python_setup_py'
+[0.354s] Level 1:colcon.colcon_core.package_identification:_identify(Blender) by extensions ['ignore', 'ignore_ament_install']
+[0.355s] Level 1:colcon.colcon_core.package_identification:_identify(Blender) by extension 'ignore'
+[0.355s] Level 1:colcon.colcon_core.package_identification:_identify(Blender) by extension 'ignore_ament_install'
+[0.355s] Level 1:colcon.colcon_core.package_identification:_identify(Blender) by extensions ['colcon_pkg']
+[0.355s] Level 1:colcon.colcon_core.package_identification:_identify(Blender) by extension 'colcon_pkg'
+[0.355s] Level 1:colcon.colcon_core.package_identification:_identify(Blender) by extensions ['colcon_meta']
+[0.355s] Level 1:colcon.colcon_core.package_identification:_identify(Blender) by extension 'colcon_meta'
+[0.355s] Level 1:colcon.colcon_core.package_identification:_identify(Blender) by extensions ['ros']
+[0.355s] Level 1:colcon.colcon_core.package_identification:_identify(Blender) by extension 'ros'
+[0.355s] Level 1:colcon.colcon_core.package_identification:_identify(Blender) by extensions ['cmake', 'python']
+[0.355s] Level 1:colcon.colcon_core.package_identification:_identify(Blender) by extension 'cmake'
+[0.355s] Level 1:colcon.colcon_core.package_identification:_identify(Blender) by extension 'python'
+[0.355s] Level 1:colcon.colcon_core.package_identification:_identify(Blender) by extensions ['python_setup_py']
+[0.355s] Level 1:colcon.colcon_core.package_identification:_identify(Blender) by extension 'python_setup_py'
+[0.355s] Level 1:colcon.colcon_core.package_identification:_identify(__pycache__) by extensions ['ignore', 'ignore_ament_install']
+[0.355s] Level 1:colcon.colcon_core.package_identification:_identify(__pycache__) by extension 'ignore'
+[0.355s] Level 1:colcon.colcon_core.package_identification:_identify(__pycache__) by extension 'ignore_ament_install'
+[0.356s] Level 1:colcon.colcon_core.package_identification:_identify(__pycache__) by extensions ['colcon_pkg']
+[0.356s] Level 1:colcon.colcon_core.package_identification:_identify(__pycache__) by extension 'colcon_pkg'
+[0.356s] Level 1:colcon.colcon_core.package_identification:_identify(__pycache__) by extensions ['colcon_meta']
+[0.356s] Level 1:colcon.colcon_core.package_identification:_identify(__pycache__) by extension 'colcon_meta'
+[0.356s] Level 1:colcon.colcon_core.package_identification:_identify(__pycache__) by extensions ['ros']
+[0.356s] Level 1:colcon.colcon_core.package_identification:_identify(__pycache__) by extension 'ros'
+[0.356s] Level 1:colcon.colcon_core.package_identification:_identify(__pycache__) by extensions ['cmake', 'python']
+[0.356s] Level 1:colcon.colcon_core.package_identification:_identify(__pycache__) by extension 'cmake'
+[0.356s] Level 1:colcon.colcon_core.package_identification:_identify(__pycache__) by extension 'python'
+[0.356s] Level 1:colcon.colcon_core.package_identification:_identify(__pycache__) by extensions ['python_setup_py']
+[0.356s] Level 1:colcon.colcon_core.package_identification:_identify(__pycache__) by extension 'python_setup_py'
+[0.356s] Level 1:colcon.colcon_core.package_identification:_identify(build) by extensions ['ignore', 'ignore_ament_install']
+[0.356s] Level 1:colcon.colcon_core.package_identification:_identify(build) by extension 'ignore'
+[0.356s] Level 1:colcon.colcon_core.package_identification:_identify(build) ignored
+[0.356s] Level 1:colcon.colcon_core.package_identification:_identify(install) by extensions ['ignore', 'ignore_ament_install']
+[0.356s] Level 1:colcon.colcon_core.package_identification:_identify(install) by extension 'ignore'
+[0.357s] Level 1:colcon.colcon_core.package_identification:_identify(install) ignored
+[0.357s] Level 1:colcon.colcon_core.package_identification:_identify(log) by extensions ['ignore', 'ignore_ament_install']
+[0.357s] Level 1:colcon.colcon_core.package_identification:_identify(log) by extension 'ignore'
+[0.357s] Level 1:colcon.colcon_core.package_identification:_identify(log) ignored
+[0.357s] Level 1:colcon.colcon_core.package_discovery:discover_packages(recursive) using defaults
+[0.357s] Level 1:colcon.colcon_core.package_discovery:discover_packages(ignore) discover
+[0.357s] Level 1:colcon.colcon_core.package_discovery:discover_packages(ignore) using defaults
+[0.357s] Level 1:colcon.colcon_core.package_discovery:discover_packages(path) discover
+[0.357s] Level 1:colcon.colcon_core.package_discovery:discover_packages(path) using defaults
+[0.380s] Level 1:colcon.colcon_core.package_discovery:discover_packages(prefix_path) check parameters
+[0.380s] Level 1:colcon.colcon_core.package_discovery:discover_packages(prefix_path) discover
+[0.383s] DEBUG:colcon.colcon_installed_package_information.package_discovery:Found 368 installed packages in /opt/ros/humble
+[0.385s] Level 1:colcon.colcon_core.package_discovery:discover_packages(prefix_path) using defaults
+[0.451s] INFO:colcon.colcon_core.executor:Executing jobs using 'parallel' executor
+[0.454s] DEBUG:colcon.colcon_parallel_executor.executor.parallel:run_until_complete
+[0.454s] DEBUG:colcon.colcon_parallel_executor.executor.parallel:closing loop
+[0.454s] DEBUG:colcon.colcon_parallel_executor.executor.parallel:loop closed
+[0.454s] DEBUG:colcon.colcon_parallel_executor.executor.parallel:run_until_complete finished with '0'
+[0.455s] DEBUG:colcon.colcon_core.event_reactor:joining thread
+[0.459s] INFO:colcon.colcon_core.plugin_system:Skipping extension 'colcon_notification.desktop_notification.terminal_notifier': Not used on non-Darwin systems
+[0.459s] INFO:colcon.colcon_core.plugin_system:Skipping extension 'colcon_notification.desktop_notification.win32': Not used on non-Windows systems
+[0.459s] INFO:colcon.colcon_notification.desktop_notification:Sending desktop notification using 'notify2'
+[0.468s] DEBUG:colcon.colcon_core.event_reactor:joined thread
+[0.472s] INFO:colcon.colcon_core.plugin_system:Skipping extension 'colcon_core.shell.bat': Not used on non-Windows systems
+[0.472s] INFO:colcon.colcon_core.shell:Creating prefix script '/home/grimmlins/Documents/GitHub/treefitting/marshall/install/local_setup.ps1'
+[0.473s] INFO:colcon.colcon_core.shell:Creating prefix util module '/home/grimmlins/Documents/GitHub/treefitting/marshall/install/_local_setup_util_ps1.py'
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+[0.475s] INFO:colcon.colcon_core.shell:Creating prefix util module '/home/grimmlins/Documents/GitHub/treefitting/marshall/install/_local_setup_util_sh.py'
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+[0.477s] INFO:colcon.colcon_core.shell:Creating prefix script '/home/grimmlins/Documents/GitHub/treefitting/marshall/install/local_setup.zsh'
+[0.478s] INFO:colcon.colcon_core.shell:Creating prefix chain script '/home/grimmlins/Documents/GitHub/treefitting/marshall/install/setup.zsh'
diff --git a/marshall/log/latest b/marshall/log/latest
new file mode 120000
index 0000000..b57d247
--- /dev/null
+++ b/marshall/log/latest
@@ -0,0 +1 @@
+latest_build
\ No newline at end of file
diff --git a/marshall/log/latest_build b/marshall/log/latest_build
new file mode 120000
index 0000000..14d2171
--- /dev/null
+++ b/marshall/log/latest_build
@@ -0,0 +1 @@
+build_2023-09-02_12-15-53
\ No newline at end of file
diff --git a/marshall/output.png b/marshall/output.png
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index 0000000..f0a2555
Binary files /dev/null and b/marshall/output.png differ
diff --git a/marshall/params.py b/marshall/params.py
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--- /dev/null
+++ b/marshall/params.py
@@ -0,0 +1,10 @@
+scale_factor = 100
+cam = 'D435_640x480.camera.npz'
+#depth_img = "depth0001.raw"
+mask_img = "leader_mask.png"
+follower_msk = "follower_mask.png"
+angle_limit = 70
+nan_value = 1
+video_file = "output.mkv"
+num_cyl = 16
+cyls = 13    #number of cylinders outputted, a set value for now but can be changed to detect it automatically from filenames
diff --git a/marshall/pull_depth_and_rgb.py b/marshall/pull_depth_and_rgb.py
new file mode 100644
index 0000000..bcb2f8f
--- /dev/null
+++ b/marshall/pull_depth_and_rgb.py
@@ -0,0 +1,28 @@
+import os
+import cv2
+
+#extracts depth and rgb data from azure kinect video
+#requires ffmpeg library: sudo apt install ffmpeg
+"""
+INSTRUCTIONS FOR RUNNING:
+1. Install ffmpeg
+2. Download folder containing video output file
+3. Copy and paste this file into the downloaded folder
+4. Navigate to downloaded folder in terminal
+5. Run script and specify filename(excluding extension) you would like to extract data from.
+"""
+print("please type the file name(excluding extension) you would like to extract from: ")
+inp = input()
+filename = f'{inp}.mkv'
+current_directory = os.getcwd()
+rgb_folder = f'{inp}_rgb_data'
+depth_folder = f'{inp}_depth_data'
+path1 = os.path.join(current_directory, rgb_folder)
+path2 = os.path.join(current_directory, depth_folder)
+os.mkdir(path1)
+os.mkdir(path2)
+
+cmd1 = f'ffmpeg -i {filename} -vf "select=not(mod(n\,10))" -map 0:0 -vsync 0 {path1}/rgb%04d.png'
+cmd2 = f'ffmpeg -i {filename} -vf "select=not(mod(n\,10))" -map 0:1 -vsync 0 {path2}/depth%04d.pgm'    #change to whichever file type is easiest to work with for depth
+os.system(cmd1)
+os.system(cmd2)