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Tweaks for better stimulus spot selection #15

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Tweaks for better stimulus spot selection #15

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14 changes: 9 additions & 5 deletions src/gui.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,12 @@ function gui(
crop_bottom::Int = 0,
crop_left::Int = 0,
crop_right::Int = 0,
min_size = 100, # minimum size of segments to keep
colorproj = RGB{Float32}(1, 1, -2), # used for identifying the stimulus
expectedpixels = 40000, # ""
expectedloc = nothing, # ""
max_size_frac = 0.1, # sets largest allowed spot size
min_size_pixels = 10 # sets smallest allowed spot size
)
channelpct(x) = string(round(Int, x * 100)) * '%'

Expand Down Expand Up @@ -122,7 +126,7 @@ function gui(
update_threshold = change -> begin
newvalue = round(threshold + change; digits=2)
try
seg = segment_image(rescaledimg; threshold = newvalue)
seg = segment_image(rescaledimg; threshold = newvalue, min_size = min_size)
nsegs = length(segment_labels(seg))
nsegs > length(colors) && @warn "More than $(length(colors)) segments ($(nsegs)). Excluded ones will be displayed in white and will not be selectable"
empty!(labels2idx)
Expand All @@ -134,7 +138,7 @@ function gui(
push!(idx2labels, idx=>l)
end
centroidsacc, _ = get_centroidsacc(seg.image_indexmap)
istim = labels2idx[stimulus_index(seg, centroidsacc; colorproj = colorproj, expectedloc = expectedloc)]
istim = labels2idx[stimulus_index(seg, centroidsacc; colorproj = colorproj, expectedpixels = expectedpixels, expectedloc = expectedloc)]
for (j, cb) in enumerate(cbs)
# set_gtk_property!(cb, "active", j <= nsegs)
cb[] = (j == istim || j == preclick)
Expand Down Expand Up @@ -182,7 +186,7 @@ function gui(
img = color.(load(file))[crop_top+1:end-crop_bottom, crop_left+1:end-crop_right]
rescaledimg = isnothing(bkgimg) ? img : (img ./ bkgimg .* bkgmean)

seg = segment_image(rescaledimg; threshold = threshold)
seg = segment_image(rescaledimg; threshold = threshold, min_size = min_size)
nsegs = length(segment_labels(seg))
nsegs > length(colors) && @warn "More than $(length(colors)) segments ($(nsegs)). Excluded ones will be displayed in white and will not be selectable"
empty!(labels2idx)
Expand All @@ -194,7 +198,7 @@ function gui(
push!(idx2labels, idx=>l)
end
centroidsacc, _ = get_centroidsacc(seg.image_indexmap)
istim = labels2idx[stimulus_index(seg, centroidsacc; colorproj = colorproj, expectedloc = expectedloc)]
istim = labels2idx[stimulus_index(seg, centroidsacc; colorproj = colorproj, expectedpixels = expectedpixels, expectedloc = expectedloc)]
for (j, cb) in enumerate(cbs)
# set_gtk_property!(cb, "active", j <= nsegs)
cb[] = (j == istim || j == preclick)
Expand All @@ -214,7 +218,7 @@ function gui(
pixelskeep = map(i -> i ∈ keep, labels_map(seg))
L = label_components(pixelskeep)
newseg = SegmentedImage(img, L)
spotdict, stimulus = spots(newseg; colorproj = colorproj, expectedloc = expectedloc)
spotdict, stimulus = spots(newseg; colorproj = colorproj, expectedpixels = expectedpixels, expectedloc = expectedloc, max_size_frac = max_size_frac, min_size_pixels = min_size_pixels)
push!(results, (file, spotdict, stimulus, newseg))
end

Expand Down
21 changes: 11 additions & 10 deletions src/segment.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ function segment_image(
img::AbstractMatrix{<:Color};
threshold::Real = 0.2, # threshold for color similarity in region growing
prune::Bool = true, # prune small segments
min_size::Int = 500, # minimum size of segments to keep
min_size::Int = 100, # minimum size of segments to keep
)
seg = unseeded_region_growing(img, threshold)
if prune
Expand All @@ -22,27 +22,27 @@ end
segment_image(img::AbstractMatrix{<:Colorant}; kwargs...) = segment_image(color.(img); kwargs...)

"""
idx = stimulus_index(seg::SegmentedImage, centroidsacc; colorproj = RGB(1, 1, -2), expectedloc = nothing)
idx = stimulus_index(seg::SegmentedImage, centroidsacc; colorproj = RGB(1, 1, -2), expectedpixels = 50000, expectedloc = nothing)

Given a segmented image `seg`, return the index of the segment that scores
highest on the product of (1) projection (dot product) with `colorproj` and (2)
number of pixels.
highest on the quotient of (1) projection (dot product) with `colorproj` with (2)
the absolute value of the difference between the number of pixels with `expectedpixels`.

Optionally, if images were taken with a fixed location for the stimulus, a segment's score
is divided by the squared distance of its centroid (via `centroidsacc`) from the position given by `expectedloc`.
"""
function stimulus_index(seg::SegmentedImage, centroidsacc; colorproj = RGB{Float32}(1, 1, -2), expectedloc = nothing)
function stimulus_index(seg::SegmentedImage, centroidsacc; colorproj = RGB{Float32}(1, 1, -2), expectedpixels = 40000, expectedloc = nothing)
if !isnothing(expectedloc)
proj = map(segment_labels(seg)) do l
l == 0 && return 0
val = centroidsacc[l]
centroid = [round(Int, val[1] / val[3]), round(Int, val[2] / val[3])]
return l => (colorproj ⋅ segment_mean(seg, l) * segment_pixel_count(seg, l) / max(1, sum(abs2, centroid .- expectedloc)))
return l => (colorproj ⋅ segment_mean(seg, l) / max(1, abs(segment_pixel_count(seg, l) - expectedpixels)) / max(1, sum(abs2, centroid .- expectedloc)))
end
(i, _) = argmax(last, proj)
return i
else
proj = [l => (colorproj ⋅ segment_mean(seg, l)) * segment_pixel_count(seg, l) for l in segment_labels(seg)]
proj = [l => (colorproj ⋅ segment_mean(seg, l)) / max(1, abs(segment_pixel_count(seg, l) - expectedpixels)) for l in segment_labels(seg)]
(i, _) = argmax(last, proj)
return i
end
Expand Down Expand Up @@ -110,18 +110,18 @@ Spots larger than `max_size_frac * npixels` (default: 10% of the image) are igno
function spots(
seg::SegmentedImage;
max_size_frac=0.1, # no spot is bigger than max_size_frac * npixels
min_size_pixels=10, # smallest allowed spot
kwargs...
)
centroidsacc, nadj = get_centroidsacc(seg.image_indexmap)
istim = stimulus_index(seg, centroidsacc; kwargs...)

stimulus = Ref{Pair{Int,Spot}}()
filter!(centroidsacc) do (key, val)
if key == istim
stimulus[] = key => Spot(val[3], (round(Int, val[1] / val[3]), round(Int, val[2] / val[3])))
return false
end
return val[3] <= max_size_frac * length(seg.image_indexmap)
return min_size_pixels <= val[3] <= max_size_frac * length(seg.image_indexmap)
# # is the centroid within the segment?
# x, y = round(Int, val[1] / val[3]), round(Int, val[2] / val[3])
# l = seg.image_indexmap[x, y]
Expand All @@ -148,6 +148,7 @@ function spots(
indexmap::Matrix{Int},
istim::Int;
max_size_frac=0.1,
min_size_pixels=10,
kwargs...
)
centroidsacc, nadj = get_centroidsacc(indexmap)
Expand All @@ -157,7 +158,7 @@ function spots(
stimulus[] = key => Spot(val[3], (round(Int, val[1] / val[3]), round(Int, val[2] / val[3])))
return false
end
return val[3] <= max_size_frac * length(indexmap)
return min_size_pixels <= val[3] <= max_size_frac * length(indexmap)
end
return Dict(l => Spot(val[3], (round(Int, val[1] / val[3]), round(Int, val[2] / val[3]))) for (l, val) in centroidsacc), stimulus[]
end
Expand Down
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