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Remove connect_eight() #122

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Mar 31, 2023
Merged

Remove connect_eight() #122

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f5308c3
Remove connect_eight()
dstansby Mar 31, 2023
ab2bae1
Fix neighbour comment
dstansby Mar 31, 2023
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87 changes: 5 additions & 82 deletions src/cellfinder_core/detect/filters/volume/structure_detection.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,8 +18,6 @@ class Point:


UINT64_MAX = np.iinfo(np.uint64).max
N_NEIGHBOURS_4_CONNECTED = 3 # below, left and behind
N_NEIGHBOURS_8_CONNECTED = 13 # all the 9 below + the 4 before on same plane


@jit(nopython=True)
Expand Down Expand Up @@ -74,7 +72,6 @@ def get_structure_centre_wrapper(structure): # wrapper for testing purposes


spec = [
("connect_type", types.uint8),
("SOMA_CENTRE_VALUE", types.uint64),
("z", types.uint64),
("relative_z", types.uint64),
Expand All @@ -88,14 +85,10 @@ def get_structure_centre_wrapper(structure): # wrapper for testing purposes

@jitclass(spec=spec)
class CellDetector:
def __init__(self, width: int, height: int, start_z: int, connect_type=4):
def __init__(self, width: int, height: int, start_z: int):
self.shape = width, height
self.z = start_z

if connect_type not in (4, 8):
raise ValueError("Connection type must be one of [4, 8]")
self.connect_type = connect_type

self.SOMA_CENTRE_VALUE = UINT64_MAX

# position to append in stack
Expand Down Expand Up @@ -138,11 +131,8 @@ def process(
elif nbits == 32:
layer *= numba.uint64(4294967297)

if self.connect_type == 4:
layer = self.connect_four(layer)
self.previous_layer = layer
else:
self.previous_layer = self.connect_eight(layer)
layer = self.connect_four(layer)
self.previous_layer = layer

if self.relative_z == 0:
self.relative_z += 1
Expand All @@ -164,10 +154,8 @@ def connect_four(self, layer):
for y in range(layer.shape[1]):
for x in range(layer.shape[0]):
if layer[x, y] == self.SOMA_CENTRE_VALUE:
# Labels of structures at left, top, below
neighbour_ids = np.zeros(
N_NEIGHBOURS_4_CONNECTED, dtype=np.uint64
)
# Labels of structures below, left and behind
neighbour_ids = np.zeros(3, dtype=np.uint64)
# If in bounds look at neighbours
if x > 0:
neighbour_ids[0] = layer[x - 1, y]
Expand All @@ -189,71 +177,6 @@ def connect_four(self, layer):

return layer

def connect_eight(self, layer):
"""
For all the pixels in the current layer, finds all structures touching
this pixel using the
eight connected (connected by edges or corners) rule and also looks at
the pixel at the same
location in the previous layer.
If structures are found, they are added to the structure manager and
the pixel labeled accordingly.

:param layer:
:return:
"""
neighbour_ids = [0] * N_NEIGHBOURS_8_CONNECTED

for y in range(layer.shape[1]):
for x in range(layer.shape[0]):
if layer[x, y] == self.SOMA_CENTRE_VALUE:
# If in bounds look at neighbours
if x > 0 and y > 0:
neighbour_ids[0] = layer[x - 1, y - 1]
if x > 0:
neighbour_ids[1] = layer[x - 1, y]
if y > 0:
neighbour_ids[2] = layer[x, y - 1]
neighbour_ids[3] = layer[x + 1, y - 1]
if self.relative_z > 0:
if x > 0 and y > 0:
neighbour_ids[4] = self.previous_layer[
x - 1, y - 1
]
if x > 0:
neighbour_ids[5] = self.previous_layer[x - 1, y]
if y < layer.shape[1] - 1:
neighbour_ids[6] = self.previous_layer[
x - 1, y + 1
]
if y > 0:
neighbour_ids[7] = self.previous_layer[x, y - 1]
if x < layer.shape[0] - 1:
neighbour_ids[8] = self.previous_layer[
x + 1, y - 1
]
neighbour_ids[9] = self.previous_layer[x, y]
if y < layer.shape[1] - 1:
neighbour_ids[10] = self.previous_layer[x, y + 1]
if x < layer.shape[0] - 1:
neighbour_ids[11] = self.previous_layer[x + 1, y]
if y < layer.shape[1] - 1:
neighbour_ids[12] = self.previous_layer[
x + 1, y + 1
]

if is_new_structure(neighbour_ids):
neighbour_ids[0] = self.next_structure_id
self.next_structure_id += 1
struct_id = self.add(x, y, self.z, neighbour_ids)
else:
# reset so that grayscale value does not count as
# structure in next iterations
struct_id = 0

layer[x, y] = struct_id
return layer

def get_cell_centres(self):
cell_centres = self.structures_to_cells()
return cell_centres
Expand Down