def i_segment_meander_angle(tree):
'''Return an iterator to a tree meander angle
The meander angle is defined as the angle between to adjacent segments.
Applies neurom.morphmath.angle_3points to triplets of
'''
return tr.imap_val(lambda t: mm.angle_3points(t[1], t[0], t[2]), tr.itriplet(tree))
def i_segment_meander_angle(tree):
'''Return an iterator to a tree meander angle
The meander angle is defined as the angle between to adjacent segments.
Applies neurom.morphmath.angle_3points to triplets of
'''
return tr.imap_val(lambda t: mm.angle_3points(t[1], t[0], t[2]),
tr.itriplet(tree))
def trunk_section_length(tree):
'''Length of the initial tree section
Returns:
Length of first section of tree or 0 if single point tree
'''
try:
_it = tr.imap_val(mm.section_length, tr.isection(tree))
return _it.next()
except StopIteration:
return 0.0
def i_segment_radial_dist(pos, tree):
'''Return an iterator of radial distances of tree segments to a given point
The radial distance is the euclidian distance between the mid-point of
the segment and the point in question.
Parameters:
pos: origin to which disrances are measured. It must have at least 3
components. The first 3 components are (x, y, z).
tree: tree of raw data rows.
'''
return tr.imap_val(lambda s: mm.segment_radial_dist(s, pos), tr.isegment(tree))
def i_segment_radial_dist(pos, tree):
'''Return an iterator of radial distances of tree segments to a given point
The radial distance is the euclidian distance between the mid-point of
the segment and the point in question.
Parameters:
pos: origin to which disrances are measured. It must have at least 3
components. The first 3 components are (x, y, z).
tree: tree of raw data rows.
'''
return tr.imap_val(lambda s: mm.segment_radial_dist(s, pos),
tr.isegment(tree))
def i_section_radial_dist(tree, pos=None, use_start_point=False):
'''Return an iterator of radial distances of tree sections to a given point
The radial distance is the euclidian distance between the either the
end-point or rhe start point of the section and the point in question.
Parameters:
tree: tree object
pos: origin to which distances are measured. It must have at least 3\
components. The first 3 components are (x, y, z).\
(default tree origin)
use_start_point: If true, calculate distance from section start point,\
else from end-point (default, False)
'''
pos = tree.value if pos is None else pos
sec_idx = 0 if use_start_point else -1
return tr.imap_val(lambda s: mm.point_dist(s[sec_idx], pos), tr.isection(tree))
def i_section_radial_dist(tree, pos=None, use_start_point=False):
'''Return an iterator of radial distances of tree sections to a given point
The radial distance is the euclidian distance between the either the
end-point or rhe start point of the section and the point in question.
Parameters:
tree: tree object
pos: origin to which distances are measured. It must have at least 3\
components. The first 3 components are (x, y, z).\
(default tree origin)
use_start_point: If true, calculate distance from section start point,\
else from end-point (default, False)
'''
pos = tree.value if pos is None else pos
sec_idx = 0 if use_start_point else -1
return tr.imap_val(lambda s: mm.point_dist(s[sec_idx], pos),
tr.isection(tree))
def i_segment_area(tree):
''' return an iterator of tree segment areas
'''
return tr.imap_val(mm.segment_area, tr.isegment(tree))
def i_segment_volume(tree):
''' return an iterator of tree segment volumes
'''
return tr.imap_val(mm.segment_volume, tr.isegment(tree))
def i_segment_radius(tree):
''' return an iterator of tree segment radii
'''
return tr.imap_val(mm.segment_radius, tr.isegment(tree))
def i_segment_length(tree):
''' return an iterator of tree segment lengths
'''
return tr.imap_val(mm.segment_length, tr.isegment(tree))
def path_length(tree):
'''Get the path length from a sub-tree to the root node'''
return np.sum(s for s in tr.imap_val(mm.segment_length,
tr.isegment(tree, tr.iupstream)))
def i_segment_area(tree):
''' return an iterator of tree segment areas
'''
return tr.imap_val(mm.segment_area, tr.isegment(tree))
def i_segment_volume(tree):
''' return an iterator of tree segment volumes
'''
return tr.imap_val(mm.segment_volume, tr.isegment(tree))
def i_segment_radius(tree):
''' return an iterator of tree segment radii
'''
return tr.imap_val(mm.segment_radius, tr.isegment(tree))
def i_segment_length(tree):
''' return an iterator of tree segment lengths
'''
return tr.imap_val(mm.segment_length, tr.isegment(tree))
def path_length(tree):
'''Get the path length from a sub-tree to the root node'''
return np.sum(s for s in
tr.imap_val(mm.segment_length, tr.isegment(tree, tr.iupstream)))
def i_section_length(tree):
"""
Return an iterator of tree section lengths
"""
return tr.imap_val(mm.section_length, tr.isection(tree))
def i_section_length(tree):
"""
Return an iterator of tree section lengths
"""
return tr.imap_val(mm.section_length, tr.isection(tree))