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Update 2017-03-15
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@jpjones76
jpjones76 committed Mar 15, 2017
1 parent d05f421 commit 16235c4
Showing 1 changed file with 35 additions and 305 deletions.
340 changes: 35 additions & 305 deletions src/Types/SeisData.jl
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Original file line number Diff line number Diff line change
@@ -1,223 +1,5 @@
<<<<<<< HEAD
import Base:in, getindex, setindex!, append!, deleteat!, delete!, +, -, *, isequal,
length, start, done, next, size, sizeof, ==, isempty, sort!, sort, endof

# This is type-stable for S = SeisData() but not for keyword args
type SeisData
n::Int64
c::Array{TCPSocket,1} # connections
name::Array{String,1} # name
id::Array{String,1} # id
loc::Array{Array{Float64,1},1} # loc
fs::Array{Float64,1} # fs
gain::Array{Float64,1} # gain
resp::Array{Array{Complex{Float64},2},1} # resp
units::Array{String,1} # units
misc::Array{Dict{String,Any},1} # misc
notes::Array{Array{String,1},1} # notes
src::Array{String,1} # src
t::Array{Array{Int64,2},1} # time
x::Array{Array{Float64,1},1} # data

function SeisData(n::Int64)
n = max(n,0)
name = Array{String,1}(n)
id = Array{String,1}(n)
notes = Array{Array{String,1},1}(n)
src = Array{String,1}(n)
misc = Array{Dict{String,Any},1}(n)
n0 = tnote("Channel initialized")
s0 = "SeisData"
for i = 1:n
name[i] = string("Channel ",i)
notes[i] = Array{String,1}([identity(n0)])
src[i] = identity(s0)
misc[i] = Dict{String,Any}()
end
new(n,
Array{TCPSocket,1}(0),
name,
collect(repeated("...YYY",n)),
collect(repeated(zeros(Float64,5),n)),
collect(repeated(0.0,n)),
collect(repeated(1.0,n)),
collect(repeated(Array{Complex{Float64}}(0,2),n)),
collect(repeated("",n)),
misc,
notes,
src,
collect(repeated(Array{Int64,2}(0,2),n)),
collect(repeated(Array{Float64,1}(0),n)))
end

function SeisData(U...)
S = SeisData()
for i = 1:1:length(U)
if typeof(U[i]) in [SeisChannel,SeisData]
append!(S, U[i])
else
warn(string("Tried to join incompatible type into SeisData at arg ", i, "; skipped."))
end
end
return S
end
end
SeisData() = SeisData(0)

# ============================================================================
# Indexing, searching, iteration, size
# s = S[j] returns a SeisChannel struct
# s = S[i:j] returns a SeisData struct
# S[i:j].foo = bar won't work
endof(S::SeisData) = S.n

function getindex(S::SeisData, J::Array{Int,1})
U = SeisData()
[setfield!(U, f, getfield(S,f)[J]) for f in datafields]
setfield!(U, :n, length(J))
return U
end
getindex(S::SeisData, J::UnitRange) = getindex(S, collect(J))

in(s::String, S::SeisData) = in(s, S.id)

"""
findid(S::SeisData, n::String)
Get the index to the first channel of S where `(S.id.==n) == true`.
"""
findid(n::String, S::SeisData) = findfirst(S.id .== n)
findid(S::SeisData, n::String) = findfirst(S.id .== n)
findid(S::SeisData, T::SeisData) = [findfirst(S.id .== T.id[i]) for i=1:1:T.n]

setindex!(S::SeisData, U::SeisData, J::Array{Int,1}) = (
[(getfield(S, f))[J] = getfield(U, f) for f in datafields];
return S)
setindex!(S::SeisData, U::SeisData, J::UnitRange) = setindex!(S, U, collect(J))
setindex!(S::SeisData, U::SeisData, j::Int) = setindex!(S, U, [j])

function isempty(S::SeisData)
if S.n == 0
return true
else
return minimum([isempty(S.x[i]) for i=1:1:S.n]::Array{Bool,1})
end
end

isequal(S::SeisData, U::SeisData) = minimum([hash(getfield(S,i))==hash(getfield(U,i)) for i in datafields]::Array{Bool,1})
==(S::SeisData, U::SeisData) = isequal(S,U)::Bool

function sizeof(S::SeisData)
N = Array{Int,1}(length(datafields))
M = Array{Int,1}(length(datafields))
[M[i] = sizeof(getfield(S,f)) for (i,f) in enumerate(datafields)]
[N[i] = sum([M[j] = sizeof(V) for (j,V) in enumerate(getfield(S,f))]) for (i,f) in enumerate(datafields)]
return sum(N) + sum(M)
end
# ============================================================================


# ============================================================================
# Annotation

# Adding a string to SeisData writes a note; if the string mentions a channel
# name or ID, the note is restricted to the given channels(s), else it's
# added to all channels
"""
note!(S::SeisData, s::String)
Append a timestamped note to `S.notes`. If `txt` mentions a channel name or ID, only the corresponding channel is annotated; otherwise, all channels are annotated.
"""
function note!(S::SeisData, s::String)
j = find(maximum([[findfirst(contains(s,i)) for i in S.name] [findfirst(contains(s,i)) for i in S.id]],2).>0)
if !isempty(j)
[push!(S.notes[i], tnote(s)) for i in j]
else
for i = 1:1:S.n
push!(S.notes[i], tnote(s))
end
end
return S
end

note!(S::SeisData, i::Integer, s::String) = push!(S.notes[i], tnote(s))

# ============================================================================
# Append, add, delete, sort
append!(S::SeisData, U::SeisData) = (
[setfield!(S, i, append!(getfield(S,i), getfield(U,i))) for i in datafields];
S.n += U.n;
return S)
+(S::SeisData, U::SeisData) = (T = deepcopy(S); return append!(T, U))

# Delete methods are aliased to -
deleteat!(S::SeisData, j::Int) = ([deleteat!(getfield(S, i),j) for i in datafields]; S.n -= 1; return S)
deleteat!(S::SeisData, J::Array{Int,1}) = (sort!(J); [deleteat!(getfield(S, f), J) for f in datafields]; S.n -= length(J))
deleteat!(S::SeisData, K::UnitRange) = (J = collect(K); deleteat!(S, J))

# With this convention, S+U-U = S
function deleteat!(S::SeisData, U::SeisData)
id = flipdim(U.id,1)
J = Array{Int64,1}(0)
for i in id
j = findlast(S.id.==i)
(j > 0) && push!(J,j)
end
deleteat!(S, J)
return nothing
end

# Delete by Regex match or exact ID match
delete!(S::SeisData, r::Regex) = deleteat!(S, find([ismatch(r, i) for i in S.id]))
delete!(S::SeisData, s::String) = (i = findlast(S.id.==s); (i > 0) && deleteat!(S, i))

# Nothing more than aliasing, really
delete!(S::SeisData, j::Int) = deleteat!(S, j)
delete!(S::SeisData, J::UnitRange) = deleteat!(S, J)
delete!(S::SeisData, J::Array{Int,1}) = deleteat!(S, J)

# Subtraction
-(S::SeisData, i::Int) = (U = deepcopy(S); deleteat!(U,i); return U) # By channel #
-(S::SeisData, J::Array{Int,1}) = (U = deepcopy(S); deleteat!(U,J); return U) # By array of channel #s
-(S::SeisData, J::Range) = (U = deepcopy(S); deleteat!(U,J); return U) # By range of channel #s
-(S::SeisData, s::String) = (U = deepcopy(S); delete!(U,s); return U) # By channel id string
-(S::SeisData, r::Regex) = (U = deepcopy(S); delete!(U,r); return U) # By channel id regex
-(S::SeisData, T::SeisData) = (U = deepcopy(S); delete!(U,T); return U) # Remove all channels in one SeisData from another

# Extract
"""
T = pull(S::SeisData, id::String)
Extract the first channel with id=`id` from `S` and return it as a new SeisData structure. The corresponding channel in `S` is deleted.
T = pull(S::SeisData, i::integer)
Extract channel `i` from `S` as a new SeisData struct, deleting it from `S`.
"""
pull(S::SeisData, s::String) = (i = findid(S, s); T = deepcopy(getindex(S, i));
deleteat!(S,i); note!(T,"Extracted from another SeisData object"); return T)
pull(S::SeisData, J::UnitRange) = (T = deepcopy(getindex(S, J)); deleteat!(S,J);
note!(T,"Extracted from a SeisData object"); return T)
pull(S::SeisData, J::Array{Integer,1}) = (T = deepcopy(getindex(S, J)); deleteat!(S,J);
note!(T,"Extracted from a SeisData object"); return T)


# Sorting
"""
sort!(S::SeisData, [rev=false])
In-place sort of channels in object S by `S.id`. Specify `rev=true` to reverse the sort order.
"""
function sort!(S::SeisData; rev=false::Bool)
j = sortperm(S.id, rev=rev)
[setfield!(S,i,getfield(S,i)[j]) for i in datafields]
return S
end
sort(S::SeisData; rev=false::Bool) = (T = deepcopy(S); j = sortperm(T.id, rev=rev); [setfield!(T,i,getfield(T,i)[j]) for i in datafields]; return(T))
=======
import Base:in, getindex, setindex!, append!, deleteat!, delete!, +, -, isequal,
merge!, merge, length, start, done, next, size, sizeof, ==, isempty, sort!, sort
import Base:in, getindex, setindex!, append!, deleteat!, delete!, +, -, *, isequal,
length, start, done, next, size, sizeof, ==, isempty, sort!, sort, endof

# This is type-stable for S = SeisData() but not for keyword args
type SeisData
Expand All @@ -243,7 +25,6 @@ type SeisData
notes = Array{Array{String,1},1}(n)
src = Array{String,1}(n)
misc = Array{Dict{String,Any},1}(n)
t = timestamp()
n0 = tnote("Channel initialized")
s0 = "SeisData"
for i = 1:n
Expand All @@ -255,7 +36,7 @@ type SeisData
new(n,
Array{TCPSocket,1}(0),
name,
collect(repeated("....",n)),
collect(repeated("...YYY",n)),
collect(repeated(zeros(Float64,5),n)),
collect(repeated(0.0,n)),
collect(repeated(1.0,n)),
Expand All @@ -272,7 +53,7 @@ type SeisData
S = SeisData()
for i = 1:1:length(U)
if typeof(U[i]) in [SeisChannel,SeisData]
merge!(S, U[i])
append!(S, U[i])
else
warn(string("Tried to join incompatible type into SeisData at arg ", i, "; skipped."))
end
Expand All @@ -287,6 +68,7 @@ SeisData() = SeisData(0)
# s = S[j] returns a SeisChannel struct
# s = S[i:j] returns a SeisData struct
# S[i:j].foo = bar won't work
endof(S::SeisData) = S.n

function getindex(S::SeisData, J::Array{Int,1})
U = SeisData()
Expand Down Expand Up @@ -361,26 +143,46 @@ end
note!(S::SeisData, i::Integer, s::String) = push!(S.notes[i], tnote(s))

# ============================================================================
# Append, delete, sort
# Append, add, delete, sort
append!(S::SeisData, U::SeisData) = (
[setfield!(S, i, append!(getfield(S,i), getfield(U,i))) for i in datafields];
S.n += U.n;
return S)
+(S::SeisData, U::SeisData) = (T = deepcopy(S); return append!(T, U))

# Delete methods are aliased to -
deleteat!(S::SeisData, j::Int) = ([deleteat!(getfield(S, i),j) for i in datafields]; S.n -= 1; return S)
deleteat!(S::SeisData, J::UnitRange) = (collect(J); [deleteat!(S, j) for j in sort(J, rev=true)]; return S)
deleteat!(S::SeisData, J::Array{Int,1}) = ([deleteat!(S, j) for j in sort(J, rev=true)]; return S)
deleteat!(S::SeisData, J::Array{Int,1}) = (sort!(J); [deleteat!(getfield(S, f), J) for f in datafields]; S.n -= length(J))
deleteat!(S::SeisData, K::UnitRange) = (J = collect(K); deleteat!(S, J))

# With this convention, S+U-U = S
function deleteat!(S::SeisData, U::SeisData)
id = flipdim(U.id,1)
J = Array{Int64,1}(0)
for i in id
j = findlast(S.id.==i)
(j > 0) && push!(J,j)
end
deleteat!(S, J)
return nothing
end

# Delete by Regex match or exact ID match
delete!(S::SeisData, r::Regex) = deleteat!(S, find([ismatch(r, i) for i in S.id]))
delete!(S::SeisData, s::String) = (i = findlast(S.id.==s); (i > 0) && deleteat!(S, i))

# Nothing more than aliasing, really
delete!(S::SeisData, j::Int) = deleteat!(S, j)
delete!(S::SeisData, J::UnitRange) = deleteat!(S, J)
delete!(S::SeisData, J::Array{Int,1}) = deleteat!(S, J)
delete!(S::SeisData, r::Regex) = deleteat!(S, find([ismatch(r, i) for i in S.id]))
delete!(S::SeisData, s::String) = delete!(S, Regex(s))
-(S::SeisData, i::Int) = deleteat!(S,i) # By channel #
-(S::SeisData, J::Array{Int,1}) = deleteat!(S,J) # By array of channel #s
-(S::SeisData, J::Range) = deleteat!(S,J) # By range of channel #s
-(S::SeisData, s::String) = delete!(S,s) # By channel id string
-(S::SeisData, r::Regex) = delete!(S,r) # By channel id regex

# Subtraction
-(S::SeisData, i::Int) = (U = deepcopy(S); deleteat!(U,i); return U) # By channel #
-(S::SeisData, J::Array{Int,1}) = (U = deepcopy(S); deleteat!(U,J); return U) # By array of channel #s
-(S::SeisData, J::Range) = (U = deepcopy(S); deleteat!(U,J); return U) # By range of channel #s
-(S::SeisData, s::String) = (U = deepcopy(S); delete!(U,s); return U) # By channel id string
-(S::SeisData, r::Regex) = (U = deepcopy(S); delete!(U,r); return U) # By channel id regex
-(S::SeisData, T::SeisData) = (U = deepcopy(S); delete!(U,T); return U) # Remove all channels in one SeisData from another

# Extract
"""
Expand Down Expand Up @@ -412,75 +214,3 @@ function sort!(S::SeisData; rev=false::Bool)
return S
end
sort(S::SeisData; rev=false::Bool) = (T = deepcopy(S); j = sortperm(T.id, rev=rev); [setfield!(T,i,getfield(T,i)[j]) for i in datafields]; return(T))

# ============================================================================
# Merge and extract
# Dealing with sparse time difference representations

"""
merge!(S::SeisData, U::SeisData)
Merge two SeisData structures. For timeseries data, a single-pass merge-and-prune operation is applied to value pairs whose sample times are separated by less than half the sampling interval; pairs of non-NaN x_i, x_j with |t_i-t_j| < (1/2*S.fs) are averaged.
`merge!` always invokes `sort!` to ensure the "+" operator is commutative.
"""
function merge!(S::SeisData, U::SeisData)
J = Array{Int64,1}()
for j = 1:1:U.n
merged = false
for i = 1:1:S.n
if S.id[i] == U.id[j]
# Merge condition: same fs, neither empty
if S.fs[i] == U.fs[j] && !isempty(U.x[j]) && !isempty(S.x[i])
x = deepcopy(U.x[j])::Array{Float64,1}
if S.gain[i] != U.gain[j]
x = x.*(S.gain[i]/U.gain[j])
end
V = xtmerge(S.t[i], U.t[j], S.x[i], x, S.fs[i])
S.t[i] = deepcopy(V[1])
S.x[i] = deepcopy(V[2])
merge!(S.misc[i], U.misc[j])
S.notes[i] = Array{String,1}([S.notes[i]; U.notes[j]])
notestr = string("Merged ", length(x), " samples")
if S.name[i] != U.name[j]
notestr = string(notestr, " (pre-merge channel name was ",U.name[j],")")
end
note!(S, i, notestr)
merged = true

# Replace an empty S.x with the corresponding U.x
elseif isempty(S.x[i])
S.x[i] = deepcopy(U.x[j])
S.t[i] = deepcopy(U.t[j])
S.fs[i] = copy(U.fs[j])
S.gain[i] = copy(U.gain[j])
merged = true

# Warn if U.x is empty, but do nothing else
elseif isempty(U.x[j])
warn(string("Trying to merge empty (dataless) channel ", U.id[j], "; ignored."))
merged = true

# Warn of possibly strange behavior with inequal fs
elseif S.fs[i] != U.fs[j]
warn(string("Tried to merge two of ", U.id[j], " with different fs values; the second will be appended."))
end
if !isempty(U.src[j])
note!(S, string("+src:", U.src[j]))
end
end
end
# If still unmerged at i=S.n, push index to J
if !merged
push!(J,j)
end
end
if !isempty(J)
append!(S, U[J])
end
return sort!(S)
end

merge(S::SeisData, U::SeisData) = (return merge!(deepcopy(S),U))
+(S::SeisData, U::SeisData) = (return merge!(S,U))
>>>>>>> b46dcd0d9ffd293c77d30a1b720c9506c2c55386

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