Glossary
===========================
.. glossary::
   :sorted:
   
   Angle
     (angle) Arctan(rise/run). Measured in radians. This is the angle of the branch with the XY plane. This angle is therefore <0 when the branch is tilted away from the tree's trunk and >0 when the branch tilted towards the trunk.
   
   Branch Order
     (branch_order) The number of junctions away from the trees' trunk. Trunk cyls have order 0, branches sprouting directly from the trunk have order 1, branches forking from order 1 branches have order 2 etc.
   
   Diameter at Breast Height
     (DBH) The diameter of the tree at a height of 1.35 meters.
   
   File Name
     (fileName) Can be thought of as the tree name; one files = one full set of cylinders for a given tree.
   
   Maximum Branch Order
     (maxBo, max_bo) The maximum branch order present in the tree   (in the cyl data).
   
   Maximum X Coordinate
     (X_max) The maximum X coordinate of the tree.
   
   Maximum Y Coordinate
     (Y_max) The maximum Y coordinate of the tree.
   
   Maximum Z Coordinate
     (Z_max) The maximum Z coordinate of the tree.
   
   Minimum X Coordinate
     (X_min) The minimum X coordinate of the tree.
   
   Minimum Y Coordinate
     (Y_min) The minimum Y coordinate of the tree.
   
   Minimum Z Coordinate
     (Z_min) The minimum Z coordinate of the tree.
   
   Number of Drip Points
     (num_drip_points) The number of points where water drips from the tree.
   
   Order One Angle Average
     (Order_one_angle_avg) The average angle of the branches with order one.
   
   Order One Angle Standard Deviation
     (Order_one_angle_std) The standard deviation of the angles of the branches with order one.
   
   Order Three Angle Average
     (Order_three_angle_avg) The average angle of the branches with order three.
   
   Order Two Angle Average
     (Order_two_angle_avg) The average angle of the branches with order two.
   
   Order Two Angle Standard Deviation
     (Order_two_angle_std) The standard deviation of the angles of the branches with order two.
   
   Order Zero Angle Average
     (Order_zero_angle_avg) The average angle of the branches with order zero.
   
   Order Zero Angle Standard Deviation
     (Order_zero_angle_std) The standard deviation of the angles of the branches with order zero.
   
   Projected Surface Area
     (total_psa) Total projected area for all cylinders of the tree.
   
   Projected Surface Area With Overlap
     (PsaWOverlap, psa_w_overlap) The sum of the projected area of each cylinder calculated independently. This is useful as it is used to exploit the fact that total_psa = psaWOverlap -   (the sum of overlapping areas of the projected cylinders). This allows us to get an estimate of what portion of the canopy is shaded.
   
   Stem Hull Area
     (stem_hull_area) Area of the alpha shape   (a tight boundary enclosing the stem) calculated for the tree.
   
   Stem Hull Boundary
     (stem_hull_boundary) The length of the perimeter of the stem alpha shape.
   
   Stem Projected Surface Area
     (stem_psa) Projected area for all cylinders of the stem.
   
   Stem Projected Surface Area With Overlap
     (stem_psa_w_overlap) The sum of the projected area of each stem cylinder calculated independently, including overlaps.
   
   Stem Surface Area
     (stem_surface_area) The sum of the non-projected/3D surface area of stem cylinders minus the areas of the top and bottom of the cylinder.
   
   Total Hull Area
     (tot_hull_area) Area of the alpha shape   (a tight boundary enclosing the canopy) calculated for the tree.
   
   Total Hull Boundary
     (tot_hull_boundary) The length of the perimeter of the alpha shape.
   
   Total Shade
     (TotalShade) PsaWOverlap - total_psa. the sum total of the area where our cylinders overlap.
   
   Total Surface Area
     (tot_surface_area) The sum of the non-projected/3D surface area of cylinders minus the areas of the top and bottom of the cylinder.
   
   Top Half Shade
     (topHalfShade, top_half_shade) See Top Quarter Shade.
   
   Top Half Total Projected Surface Area
     (topHalfTotPsa) The projected area of all cylinders in the top 50% of the canopy.
   
   Top Quarter Shade
     (topQuarterShade, top_quarter_shade) Total overlap area in the top 25% of the canopy; estimates the total shaded area   (area of diffuse v. direct sunlight) in the highest 25% of the tree.
   
   Top Quarter Total Projected Surface Area
     (topQuarterTotPsa) The projected area of all cylinders in the top 25% of the canopy.
   
   Top Three Quarter Shade
     (topThreeQuarterShade, top_three_quarter_shade) See Top Quarter Shade.
   
   Top Three Quarter Total Projected Surface Area
     (topThreeQuarterTotPsa) The projected area of all cylinders in the top 75% of the canopy.
   
   Volume
     (volume) The sum of the volumes of each cylinder.