/
_ccomp.pyx
740 lines (610 loc) · 26.6 KB
/
_ccomp.pyx
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#cython: cdivision=True
#cython: boundscheck=False
#cython: nonecheck=False
#cython: wraparound=False
import numpy as np
cimport numpy as cnp
cnp.import_array()
DTYPE = np.intp
cdef DTYPE_t BG_NODE_NULL = -999
cdef struct s_shpinfo
ctypedef s_shpinfo shape_info
ctypedef size_t (* fun_ravel)(size_t, size_t, size_t, shape_info *) noexcept nogil
# For having stuff concerning background in one place
ctypedef struct bginfo:
## The value in the image (i.e. not the label!) that identifies
## the background.
DTYPE_t background_val
DTYPE_t background_node
## Identification of the background in the labelled image
DTYPE_t background_label
cdef void get_bginfo(background_val, bginfo *ret) except *:
if background_val is None:
ret.background_val = 0
else:
ret.background_val = background_val
# The node -999 doesn't exist, it will get substituted by a meaningful value
# upon the first background pixel occurrence
ret.background_node = BG_NODE_NULL
ret.background_label = 0
# A pixel has neighbors that have already been scanned.
# In the paper, the pixel is denoted by E and its neighbors:
#
# z=1 z=0 x
# ---------------------->
# | A B C F G H
# | D E . I J K
# | . . . L M N
# |
# y V
#
# D_ea represents offset of A from E etc. - see the definition of
# get_shape_info
cdef enum:
# the 0D neighbor
# D_ee, # We don't need D_ee
# the 1D neighbor
D_ed,
# 2D neighbors
D_ea, D_eb, D_ec,
# 3D neighbors
D_ef, D_eg, D_eh, D_ei, D_ej, D_ek, D_el, D_em, D_en,
D_COUNT
# Structure for centralized access to shape data
# Contains information related to the shape of the input array
cdef struct s_shpinfo:
DTYPE_t x
DTYPE_t y
DTYPE_t z
# Number of elements
DTYPE_t numels
# Dimensions of of the input array
DTYPE_t ndim
# Offsets between elements recalculated to linear index increments
# DEX[D_ea] is offset between E and A (i.e. to the point to upper left)
# The name DEX is supposed to evoke DE., where . = A, B, C, D, F etc.
DTYPE_t DEX[D_COUNT]
# Function pointer to a function that recalculates multi-index to linear
# index. Heavily depends on dimensions of the input array.
fun_ravel ravel_index
cdef void get_shape_info(inarr_shape, shape_info *res) except *:
"""
Precalculates all the needed data from the input array shape
and stores them in the shape_info struct.
"""
res.y = 1
res.z = 1
res.ravel_index = ravel_index2D
# A shape (3, 1, 4) would make the algorithm crash, but the corresponding
# good_shape (i.e. the array with axis swapped) (1, 3, 4) is OK.
# Having an axis length of 1 when an axis on the left is longer than 1
# (in this case, it has length of 3) is NOT ALLOWED.
good_shape = tuple(sorted(inarr_shape))
res.ndim = len(inarr_shape)
if res.ndim == 1:
res.x = inarr_shape[0]
res.ravel_index = ravel_index1D
elif res.ndim == 2:
res.x = inarr_shape[1]
res.y = inarr_shape[0]
res.ravel_index = ravel_index2D
if res.x == 1 and res.y > 1:
# Should not occur, but better be safe than sorry
raise ValueError(
"Swap axis of your %s array so it has a %s shape"
% (inarr_shape, good_shape))
elif res.ndim == 3:
res.x = inarr_shape[2]
res.y = inarr_shape[1]
res.z = inarr_shape[0]
res.ravel_index = ravel_index3D
if ((res.x == 1 and res.y > 1)
or res.y == 1 and res.z > 1):
# Should not occur, but better be safe than sorry
raise ValueError(
"Swap axes of your %s array so it has a %s shape"
% (inarr_shape, good_shape))
else:
raise NotImplementedError(
"Only for images of dimension 1-3 are supported, got a %sD one"
% res.ndim)
res.numels = res.x * res.y * res.z
# When reading this for the first time, look at the diagram by the enum
# definition above (keyword D_ee)
# Difference between E and G is (x=0, y=-1, z=-1), E and A (-1, -1, 0) etc.
# Here, it is recalculated to linear (raveled) indices of flattened arrays
# with their last (=contiguous) dimension is x.
# So now the 1st (needed for 1D, 2D and 3D) part, y = 1, z = 1
res.DEX[D_ed] = -1
# Not needed, just for illustration
# res.DEX[D_ee] = 0
# So now the 2nd (needed for 2D and 3D) part, y = 0, z = 1
res.DEX[D_ea] = res.ravel_index(-1, -1, 0, res)
res.DEX[D_eb] = res.DEX[D_ea] + 1
res.DEX[D_ec] = res.DEX[D_eb] + 1
# And now the 3rd (needed only for 3D) part, z = 0
res.DEX[D_ef] = res.ravel_index(-1, -1, -1, res)
res.DEX[D_eg] = res.DEX[D_ef] + 1
res.DEX[D_eh] = res.DEX[D_ef] + 2
res.DEX[D_ei] = res.DEX[D_ef] - res.DEX[D_eb] # DEX[D_eb] = one row up, remember?
res.DEX[D_ej] = res.DEX[D_ei] + 1
res.DEX[D_ek] = res.DEX[D_ei] + 2
res.DEX[D_el] = res.DEX[D_ei] - res.DEX[D_eb]
res.DEX[D_em] = res.DEX[D_el] + 1
res.DEX[D_en] = res.DEX[D_el] + 2
cdef inline void join_trees_wrapper(DTYPE_t *data_p, DTYPE_t *forest_p,
DTYPE_t rindex, DTYPE_t idxdiff) noexcept nogil:
if data_p[rindex] == data_p[rindex + idxdiff]:
join_trees(forest_p, rindex, rindex + idxdiff)
cdef size_t ravel_index1D(size_t x, size_t y, size_t z,
shape_info *shapeinfo) noexcept nogil:
"""
Ravel index of a 1D array - trivial. y and z are ignored.
"""
return x
cdef size_t ravel_index2D(size_t x, size_t y, size_t z,
shape_info *shapeinfo) noexcept nogil:
"""
Ravel index of a 2D array. z is ignored
"""
cdef size_t ret = x + y * shapeinfo.x
return ret
cdef size_t ravel_index3D(size_t x, size_t y, size_t z,
shape_info *shapeinfo) noexcept nogil:
"""
Ravel index of a 3D array
"""
cdef size_t ret = x + y * shapeinfo.x + z * shapeinfo.y * shapeinfo.x
return ret
# Tree operations implemented by an array as described in Wu et al.
# The term "forest" is used to indicate an array that stores one or more trees
# Consider a following tree:
#
# 5 ----> 3 ----> 2 ----> 1 <---- 6 <---- 7
# | |
# 4 >----/ \----< 8 <---- 9
#
# The vertices are a unique number, so the tree can be represented by an
# array where a the tuple (index, array[index]) represents an edge,
# so for our example, array[2] == 1, array[7] == 6 and array[1] == 1, because
# 1 is the root.
# Last but not least, one array can hold more than one tree as long as their
# indices are different. It is the case in this algorithm, so for that reason
# the array is referred to as the "forest" = multiple trees next to each
# other.
#
# In this algorithm, there are as many indices as there are elements in the
# array to label and array[x] == x for all x. As the labelling progresses,
# equivalence between so-called provisional (i.e. not final) labels is
# discovered and trees begin to surface.
# When we found out that label 5 and 3 are the same, we assign array[5] = 3.
cdef DTYPE_t find_root(DTYPE_t *forest, DTYPE_t n) noexcept nogil:
"""Find the root of node n.
Given the example above, for any integer from 1 to 9, 1 is always returned
"""
cdef DTYPE_t root = n
while (forest[root] < root):
root = forest[root]
return root
cdef inline void set_root(DTYPE_t *forest, DTYPE_t n, DTYPE_t root) noexcept nogil:
"""
Set all nodes on a path to point to new_root.
Given the example above, given n=9, root=6, it would "reconnect" the tree.
so forest[9] = 6 and forest[8] = 6
The ultimate goal is that all tree nodes point to the real root,
which is element 1 in this case.
"""
cdef DTYPE_t j
while (forest[n] < n):
j = forest[n]
forest[n] = root
n = j
forest[n] = root
cdef inline void join_trees(DTYPE_t *forest, DTYPE_t n, DTYPE_t m) noexcept nogil:
"""Join two trees containing nodes n and m.
If we imagine that in the example tree, the root 1 is not known, we
rather have two disjoint trees with roots 2 and 6.
Joining them would mean that all elements of both trees become connected
to the element 2, so forest[9] == 2, forest[6] == 2 etc.
However, when the relationship between 1 and 2 can still be discovered later.
"""
cdef DTYPE_t root
cdef DTYPE_t root_m
if (n != m):
root = find_root(forest, n)
root_m = find_root(forest, m)
if (root > root_m):
root = root_m
set_root(forest, n, root)
set_root(forest, m, root)
def _get_swaps(shp):
"""
What axes to swap if we want to convert an illegal array shape
to a legal one.
Args:
shp (tuple-like): The array shape
Returns:
list: List of tuples to be passed to np.swapaxes
"""
shp = np.array(shp)
swaps = []
# Dimensions where the array is "flat"
ones = np.where(shp == 1)[0][::-1]
# The other dimensions
bigs = np.where(shp > 1)[0]
# We now go from opposite directions and swap axes if an index of a flat
# axis is higher than the one of a thick axis
for one, big in zip(ones, bigs):
if one < big:
# We are ordered already
break
else:
swaps.append((one, big))
# TODO: Add more swaps so the array is longer along x and shorter along y
return swaps
def _apply_swaps(arr, swaps):
arr2 = arr
for one, two in swaps:
arr2 = arr.swapaxes(one, two)
return arr2
def reshape_array(arr):
"""
"Rotates" the array so it gains a shape that the algorithm can work with.
An illegal shape is (3, 1, 4), and correct one is (1, 3, 4) or (1, 4, 3).
The point is to have all 1s of the shape at the beginning, not in the
middle of the shape tuple.
Note: The greater-than-one shape component should go from greatest to
lowest numbers since it is more friendly to the CPU cache (so (1, 3, 4) is
less optimal than (1, 4, 3). Keyword to this is "memory spatial locality"
Args:
arr (np.ndarray): The array we want to fix
Returns:
tuple (result, swaps): The result is the "fixed" array and a record
of what has been done with it.
"""
swaps = _get_swaps(arr.shape)
reshaped = _apply_swaps(arr, swaps)
return reshaped, swaps
def undo_reshape_array(arr, swaps):
"""
Does the opposite of what :func:`reshape_array` does
Args:
arr (np.ndarray): The array to "revert"
swaps (list): The second result of :func:`reshape_array`
Returns:
np.ndarray: The array of the original shape
"""
# It is safer to undo axes swaps in the opposite order
# than the application order
reshaped = _apply_swaps(arr, swaps[::-1])
return reshaped
def label_cython(input_, background=None, return_num=False,
connectivity=None):
# Connected components search as described in Fiorio et al.
# We have to ensure that the shape of the input can be handled by the
# algorithm. The input is reshaped as needed for compatibility.
input_, swaps = reshape_array(input_)
shape = input_.shape
ndim = input_.ndim
cdef cnp.ndarray[DTYPE_t, ndim=1] forest
# Having data a 2D array slows down access considerably using linear
# indices even when using the data_p pointer :-(
# np.array makes a copy so it is safe to modify data in-place
data = np.array(input_, order='C', dtype=DTYPE)
forest = np.arange(data.size, dtype=DTYPE)
cdef DTYPE_t *forest_p = <DTYPE_t*>forest.data
cdef DTYPE_t *data_p = <DTYPE_t*>cnp.PyArray_DATA(data)
cdef shape_info shapeinfo
cdef bginfo bg
get_shape_info(shape, &shapeinfo)
get_bginfo(background, &bg)
if connectivity is None:
# use the full connectivity by default
connectivity = ndim
if not 1 <= connectivity <= ndim:
raise ValueError(
f'Connectivity for {input_.ndim}D image should '
f'be in [1, ..., {input_.ndim}]. Got {connectivity}.'
)
cdef DTYPE_t conn = connectivity
# Label output
cdef DTYPE_t ctr
with nogil:
scanBG(data_p, forest_p, &shapeinfo, &bg)
# the data are treated as degenerated 3D arrays if needed
# without any performance sacrifice
scan3D(data_p, forest_p, &shapeinfo, &bg, conn)
ctr = resolve_labels(data_p, forest_p, &shapeinfo, &bg)
# Work around a bug in ndimage's type checking on 32-bit platforms
if data.dtype == np.int32:
data = data.view(np.int32)
if swaps:
data = undo_reshape_array(data, swaps)
if return_num:
return data, ctr
else:
return data
cdef DTYPE_t resolve_labels(DTYPE_t *data_p, DTYPE_t *forest_p,
shape_info *shapeinfo, bginfo *bg) noexcept nogil:
"""
We iterate through the provisional labels and assign final labels based on
our knowledge of prov. labels relationship.
We also track how many distinct final labels we have.
"""
cdef DTYPE_t counter = 1, i
for i in range(shapeinfo.numels):
if i == forest_p[i]:
# We have stumbled across a root which is something new to us (root
# is the LOWEST of all prov. labels that are equivalent to it)
# If the root happens to be the background,
# assign the background label instead of a
# new label from the counter
if i == bg.background_node:
# Also, if there is no background in the image,
# bg.background_node == BG_NODE_NULL < 0 and this never occurs.
data_p[i] = bg.background_label
else:
data_p[i] = counter
# The background label is basically hardcoded to 0, so no need
# to check that the new counter != bg.background_label
counter += 1
else:
data_p[i] = data_p[forest_p[i]]
return counter - 1
cdef void scanBG(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
bginfo *bg) noexcept nogil:
"""
Settle all background pixels now and don't bother with them later.
Since this only requires one linear sweep through the array, it is fast
and it makes sense to do it separately.
The purpose of this function is update of forest_p and bg parameter inplace.
"""
cdef DTYPE_t i, bgval = bg.background_val, firstbg = shapeinfo.numels
# We find the provisional label of the background, which is the index of
# the first background pixel
for i in range(shapeinfo.numels):
if data_p[i] == bgval:
firstbg = i
bg.background_node = firstbg
break
# There is no background, therefore the first background element
# is not defined.
# Since BG_NODE_NULL < 0, this is enough to ensure
# that resolve_labels doesn't worry about background.
if bg.background_node == BG_NODE_NULL:
return
# And then we apply this provisional label to the whole background
for i in range(firstbg, shapeinfo.numels):
if data_p[i] == bgval:
forest_p[i] = firstbg
# Here, we work with flat arrays regardless whether the data is 1, 2 or 3D.
# The lookup to the neighbor in a 2D array is achieved by precalculating an
# offset and adding it to the index.
# The forward scan mask looks like this (the center point is actually E):
# (take a look at shape_info docs for more exhaustive info)
# A B C
# D E
#
# So if I am in the point E and want to take a look to A, I take the index of
# E and add shapeinfo.DEX[D_ea] to it and get the index of A.
# The 1D indices are "raveled" or "linear", that's where "rindex" comes from.
cdef void scan1D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
bginfo *bg, DTYPE_t connectivity, DTYPE_t y, DTYPE_t z) noexcept nogil:
"""
Perform forward scan on a 1D object, usually the first row of an image
"""
if shapeinfo.numels == 0:
return
# Initialize the first row
cdef DTYPE_t x, rindex, bgval = bg.background_val
cdef DTYPE_t *DEX = shapeinfo.DEX
rindex = shapeinfo.ravel_index(0, y, z, shapeinfo)
for x in range(1, shapeinfo.x):
rindex += 1
# Handle the first row
if data_p[rindex] == bgval:
# Nothing to do if we are background
continue
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
cdef void scan2D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
bginfo *bg, DTYPE_t connectivity, DTYPE_t z) noexcept nogil:
"""
Perform forward scan on a 2D array.
"""
if shapeinfo.numels == 0:
return
cdef DTYPE_t x, y, rindex, bgval = bg.background_val
cdef DTYPE_t *DEX = shapeinfo.DEX
scan1D(data_p, forest_p, shapeinfo, bg, connectivity, 0, z)
for y in range(1, shapeinfo.y):
# BEGINNING of x = 0
rindex = shapeinfo.ravel_index(0, y, 0, shapeinfo)
# Handle the first column
if data_p[rindex] != bgval:
# Nothing to do if we are background
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
# END of x = 0
for x in range(1, shapeinfo.x - 1):
# We have just moved to another column (of the same row)
# so we increment the raveled index. It will be reset when we get
# to another row, so we don't have to worry about altering it here.
rindex += 1
if data_p[rindex] == bgval:
# Nothing to do if we are background
continue
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
# Finally, the last column
# BEGINNING of x = max
rindex += 1
if data_p[rindex] != bgval:
# Nothing to do if we are background
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
# END of x = max
cdef void scan3D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
bginfo *bg, DTYPE_t connectivity) noexcept nogil:
"""
Perform forward scan on a 3D array.
"""
if shapeinfo.numels == 0:
return
cdef DTYPE_t x, y, z, rindex, bgval = bg.background_val
cdef DTYPE_t *DEX = shapeinfo.DEX
# Handle first plane
scan2D(data_p, forest_p, shapeinfo, bg, connectivity, 0)
for z in range(1, shapeinfo.z):
# Handle first row in 3D manner
# BEGINNING of y = 0
# BEGINNING of x = 0
rindex = shapeinfo.ravel_index(0, 0, z, shapeinfo)
if data_p[rindex] != bgval:
# Nothing to do if we are background
# Now we have pixels below
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
# END of x = 0
for x in range(1, shapeinfo.x - 1):
rindex += 1
# Handle the first row
if data_p[rindex] == bgval:
# Nothing to do if we are background
continue
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_el])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
# BEGINNING of x = max
rindex += 1
# Handle the last element of the first row
if data_p[rindex] != bgval:
# Nothing to do if we are background
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_el])
# END of x = max
# END of y = 0
# BEGINNING of y = ...
for y in range(1, shapeinfo.y - 1):
# BEGINNING of x = 0
rindex = shapeinfo.ravel_index(0, y, z, shapeinfo)
# Handle the first column in 3D manner
if data_p[rindex] != bgval:
# Nothing to do if we are background
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eh])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
# END of x = 0
# Handle the rest of columns
for x in range(1, shapeinfo.x - 1):
rindex += 1
if data_p[rindex] == bgval:
# Nothing to do if we are background
continue
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ef])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eh])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_el])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
# BEGINNING of x = max
rindex += 1
if data_p[rindex] != bgval:
# Nothing to do if we are background
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ef])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_el])
# END of x = max
# END of y = ...
# BEGINNING of y = max
# BEGINNING of x = 0
rindex = shapeinfo.ravel_index(0, shapeinfo.y - 1, z, shapeinfo)
# Handle the first column in 3D manner
if data_p[rindex] != bgval:
# Nothing to do if we are background
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eh])
# END of x = 0
# Handle the rest of columns
for x in range(1, shapeinfo.x - 1):
rindex += 1
if data_p[rindex] == bgval:
# Nothing to do if we are background
continue
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ef])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eh])
# BEGINNING of x = max
rindex += 1
if data_p[rindex] != bgval:
# Nothing to do if we are background
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
if connectivity >= 2:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
if connectivity >= 3:
join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ef])
# END of x = max
# END of y = max