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Some cleaning up
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@chenspc
chenspc committed Jan 5, 2020
1 parent ad9acfe commit 2f1dbbc
Showing 1 changed file with 0 additions and 164 deletions.
164 changes: 0 additions & 164 deletions src/defects.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,6 @@ export make_gpolygon!
export link_bond_polygons!
export make_signature
export make_signature!
# export is_stonewales_bond
# export is_5775_bond
# export is_stonewales
export common_members
export common_relatives
export find_defect
Expand All @@ -21,11 +18,9 @@ export find_5775
export find_divacancy
export find_flower
export find_butterfly
# export make_defect
export filter_relatives_by_type
export filter_members_by_type
export stepout
# export display_dfb

function make_graphene(atom_xy; image_sampling=1, max_bondlength=10.0, frame=1, dataset="dataset")

Expand Down Expand Up @@ -158,12 +153,6 @@ function find_stonewales(graphene, area)
return defects
end
find_stonewales(graphene) = find_stonewales(graphene, graphene)
# function is_stonewales_bond(graphene, g)
# condition1 = get_signature(g) == "7-2|"
# condition2 = get_type(g) == "Bond"
# condition3 = unique(get_signature.(filter_relatives_by_type(graphene, g, "Atom"))) == ["5-1|7-2|"]
# condition1 && condition2 && condition3
# end

function find_5775(graphene, area)
defects = GDefect[]
Expand All @@ -183,17 +172,6 @@ function find_5775(graphene, area)
return defects
end
find_5775(graphene) = find_5775(graphene, graphene)
# function is_5775_bond(graphene, g)
# condition1 = get_signature(g) == "7-2|"
# condition2 = get_type(g) == "Bond"
# key_gatoms = filter_relatives_by_type(graphene, g, "Atom")
# condition3 = unique(get_signature.(key_gatoms)) == ["6-1|7-2|"]
# gpolygon_members = filter_relatives_by_type(graphene, g, "Polygon")
# condition4 = unique(get_signature.(gpolygon_members)) == ["5-1|6-5|7-1|"]
# key_gpolygons = filter(x -> get_noa(x) == 6, vcat([filter_relatives_by_type(graphene, x, "Polygon") for x in key_gatoms]...))
# condition5 = unique(get_signature.(key_gpolygons)) == ["5-1|6-3|7-2|"]
# condition1 && condition2 && condition3 && condition4 && condition5
# end

function find_divacancy(graphene, area)
defects = GDefect[]
Expand Down Expand Up @@ -280,30 +258,6 @@ function find_defect(graphene, type::String)
end
return defects
end
# function find_defect(graphene, type::String)
# id_offset = maximum(get_id.(graphene))
# if type == "Stone-Wales"
# markers = filter(x -> is_stonewales_bond(graphene, x), graphene)
# elseif type == "5775"
# markers = filter(x -> is_5775_bond(graphene, x), graphene)
# else
# if type == "Flower"
# type_signature = "7-3|"
# gtype = "Atom"
# elseif type == "Butterfly"
# type_signature = "5-2|7-4|"
# gtype = "Polygon"
# elseif type == "Divacancy"
# type_signature = "5-2|6-6|"
# gtype = "Polygon"
# else
# type_signature = ""
# gtype = ""
# end
# markers = filter(x -> get_signature(x) == type_signature && get_type(x) == gtype, graphene)
# end
# map(x -> make_defect(graphene, markers[x], id_offset+x), collect(1:length(markers)))
# end

function find_defect(graphene, types...)
id_offset = maximum(get_id.(graphene))
Expand All @@ -314,83 +268,6 @@ function find_defect(graphene, types...)
return defects
end

# function make_defect(graphene, marker, id)
# if get_type(marker) == "Atom"
# gbond_members = filter_relatives_by_type(graphene, marker, "Bond")
# gatom_members = vcat([filter_relatives_by_type(graphene, x, "Atom") for x in gbond_members]...)
# gpolygon_members = vcat([filter_relatives_by_type(graphene, x, "Polygon") for x in gatom_members]...)
# if get_signature(marker) == "7-3|"
# type = "Flower"
# else
# type = "Complex"
# end
# elseif get_type(marker) == "Bond"
# gatom_members = filter_relatives_by_type(graphene, marker, "Atom")
# if get_signature(marker) == "7-2|"
# if unique(get_signature.(gatom_members)) == ["5-1|7-2|"]
# gpolygon_members = filter_relatives_by_type(graphene, marker, "Polygon")
# gpolygon_members = vcat([filter_relatives_by_type(graphene, x, "Polygon") for x in gatom_members]...)
# relatives = setdiff(vcat([filter_relatives_by_type(graphene, x, "Polygon") for x in gpolygon_members]...), gpolygon_members)
# # if unique(get_noa.(relatives)) == [6]
# type = "Stone-Wales"
# else
# type = "Complex"
# end
# if unique(get_signature.(gatom_members)) == ["6-1|7-2|"]
# gpolygon_members = filter_relatives_by_type(graphene, marker, "Polygon")
# gpolygon_members = vcat([filter_relatives_by_type(graphene, x, "Polygon") for x in gpolygon_members]...) |> unique
# filter!(x -> get_noa(x) != 6 , gpolygon_members)
# relatives = setdiff(vcat([filter_relatives_by_type(graphene, x, "Polygon") for x in gpolygon_members]...), gpolygon_members)
# type = "5775"
# end
# else
# type = "Complex"
# end
# elseif get_type(marker) == "Polygon"
# if get_signature(marker) == "5-2|7-4|"
# gatom_members = filter_relatives_by_type(graphene, marker, "Atom")
# gbond_members = vcat([filter_relatives_by_type(graphene, x, "Bond") for x in gatom_members]...) |> unique
# gbond_members = vcat(filter(x -> get_signature(x) == "7-2|" , gbond_members), filter_relatives_by_type(graphene, marker, "Bond"))
# gatom_members = vcat([filter_relatives_by_type(graphene, x, "Atom") for x in gbond_members]...) |> unique
# gpolygon_members = vcat([filter_relatives_by_type(graphene, x, "Polygon") for x in gatom_members]...) |> unique
# type = "Butterfly"
# elseif get_signature(marker) == "5-2|6-6|"
# gatom_members = filter!(x -> get_signature(x) == "6-2|8-1|", filter_relatives_by_type(graphene, marker, "Atom"))
# gpolygon_members = vcat(filter_relatives_by_type(graphene, marker, "Polygon"), marker)
# filter!(x -> get_noa(x) != 6 , gpolygon_members)
# if length(gatom_members) == 4
# points = map(a -> Point2D(get_x(a), get_y(a)), gatom_members)
# line_points = map(a -> Point2D(get_x(a), get_y(a)), filter(x -> get_noa(x) == 5, gpolygon_members))
# line = Line(line_points...)
# points_orientation = map(x -> orientation(line, x), points)
# if +(points_orientation...) == 0 || *(points_orientation...) == 1
# type = "Divacancy"
# else
# type = "Complex"
# end
# else
# type = "Complex"
# end
# else
# type = "Complex"
# end
# else
# gpolygon_members = filter_relatives_by_type(graphene, marker, "Polygon")
# type = "Complex"
# end
#
# gatom_gbond_members = vcat([filter_relatives_by_type(graphene, x, "Atom", "Bond") for x in gpolygon_members]...) |> unique
# members = Set(get_id.(vcat(gpolygon_members, gatom_gbond_members)))
# relatives = setdiff(vcat([filter_relatives_by_type(graphene, x, "Polygon") for x in gpolygon_members]...), gpolygon_members)
# noa = length(unique(filter(isatom, graphene[collect(members)])))
# signature = ""
# if unique(get_noa.(relatives)) != [6]
# type = "Complex"
# end
#
# GDefect(id, get_x(marker), get_y(marker), Set(get_id.(relatives)), signature, get_frame(marker), get_dataset(marker), noa, members, type)
# end

function filter_relatives_by_type(graphene, g, type)
relatives = graphene[collect(get_relatives(g))]
filter(x -> get_type(x) == type, relatives)
Expand Down Expand Up @@ -451,44 +328,3 @@ end
stepout(graphene, g, steps::Vector{String}; id=0) = stepout(graphene, g, 0, steps; id=id)
stepout(graphene, g, steps::String; id=0) = stepout(graphene, g, 0, [steps]; id=id)
stepout(graphene, g; id=0) = stepout(graphene, g, 1; id=id)


# function find_dfb_save(graphene_stack, output_path)
# divacancy = merge_stack(map(x -> find_isolated_defect(x, "divacancy"), graphene_stack))
# flower = merge_stack(map(x -> find_isolated_defect(x, "flower"), graphene_stack))
# butterfly = merge_stack(map(x -> find_isolated_defect(x, "butterfly"), graphene_stack))
# dfb = merge_stack([divacancy, flower, butterfly])
# FileIO.save(output_path, dfb)
# end
#
# function display_dfb(d_divacancy_merge, d_flower_merge, d_butterfly_merge; shape="")
# red_line = zeros(10000)
# green_line = zeros(10000)
# blue_line = zeros(10000)
# red_countmap = if ~isempty(d_divacancy_merge) countmap(DataFrame(d_divacancy_merge)[:, :frame]) else [] end
# green_countmap = if ~isempty(d_flower_merge) countmap(DataFrame(d_flower_merge)[ :, :frame]) else [] end
# blue_cpoPolygon = if ~isempty(d_butterfly_merge) countmap(DataFrame(d_butterfly_merge)[:, :frame]) else [] end
#
# for (k, v) in red_countmap
# red_line[k] = v
# end
# for (k, v) in green_countmap
# green_line[k] = v
# end
# for (k, v) in blue_countmap
# blue_line[k] = v
# end
#
# if shape == "line"
# red = red_line
# green = green_line
# blue = blue_line
# else
# red = reshape(red_line, (100, 100))
# green = reshape(green_line, (100, 100))
# blue = reshape(blue_line, (100, 100))
# end
#
# rgb_dfb = cat(red, green, blue; dims=3)
# colorview(RGB, permutedims(rgb_dfb, (3,2,1)))
# end

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