Revision

**27fa41066bf09a3c1ca00fd333f72755e481b16f**authored by H.F on**13 April 2021, 10:57 UTC**, committed by H.F on**13 April 2021, 10:57 UTC****1 parent**f3455fe

deprecations.jl

```
"""
Using given mask to export roi of cell
"""
function export_cell(track, imgs, edge_mask)
height, width = size(imgs[:,:,1]);
crop_img = zeros(700, 700, length(track)*20);
for t in 1:length(track)
x, y = Int.(floor.(track[t]));
xmin, xmax, ymin, ymax = x-349 , x+350, y-349, y+350
if xmin < 1
xmax = xmax - xmin + 1
xmin = 1
end
if xmax > 1900
xmin = xmin - (xmax-1900)
xmax = 1900
end
if ymin < 1
ymax = ymax - ymin +1
ymin = 1
end
if ymax > 1300
ymin = ymin - (ymax-1300)
ymax = 1300
end
masked_cell= (edge_mask[:,:,t] .== edge_mask[x, y, t] )
for i in 1:20
crop_img[:,:,20*(t-1)+i] =(masked_cell.*imgs[:,:,20*(t-1)+i])[xmin:xmax, ymin:ymax]
end
end
crop_img;
end
# TODO: run again and again until best fitting
"""
Extract nucleus from sperated cell
"""
function extract_nucleus( img, watershed_segments::SegmentedImage{Array{Int64,2},Float64} )
img_clear = zeros(N0f16, size(watershed_segments.image_indexmap));
img_blur = imfilter(img, Kernel.gaussian(9));
for label in watershed_segments.segment_labels
cell = img_blur .* (watershed_segments.image_indexmap .== label);
# only select 70% brigter region or fixed area
gmm = GMM(3, [pixel for pixel in real(cell) if pixel > 1e-5]);
nucleus_th = sort(gmm.μ, dims=1)[end-1];
img_clear .+= ( remove_small_area(cell .> nucleus_th)) .*img;
end
img_clear;
end#
"""
Choose cloest neighborhood
"""
function find_nearest(root, next_level, maxdistance)
nucleus_distance = [sum(abs.(root .- next_level[i])) for i in 1:length(next_level)]
mindist, mindist_index = findmin(nucleus_distance);
if mindist < maxdistance
return mindist_index
else
return nothing
end
end
"""
Find every child with given root
"""
function buildtree(root::Int, position)
tree = []
height = length(position)
level = 2
child = find_nearest(position[1][root], position[level], 100);
while( child ≠ nothing && level<height)
push!(tree, child)
child = find_nearest(position[level][child], position[level+=1], 100)
#print("$level ")
end
tree
end
"""
Extract long-life path
"""
function generate_path(pos_map)
all_path = []
for root in 1:length(pos_map[1])
tree = buildtree(root, pos_map);
if length(tree) > 70
path = [pos_map[i+1][tree[i]] for i in 1:length(tree) ];
push!(all_path, path)
end
end
all_path;
end
```

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