removed dependency on SeisIO (#113)

Project.toml

@@ -14,7 +14,7 @@ Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
-SeisIO = "b372bb87-02dd-52bb-bcf6-c30dd83fd342"
+SeisBase = "8b7dfb90-41a7-4c72-9751-87603311c074"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
@@ -28,6 +28,6 @@ GPUArrays = "3.1, 4.0, 5.0, 6.2, 7.0, 8.0"
 Glob = "1.2"
 JLD2 = "0.1, 0.2, 0.3, 0.4"
 RecipesBase = "1.1"
-SeisIO = "1.0, 1.1, 1.2"
+SeisBase = "0.1.0"
 StatsBase = "0.32,0.33"
 julia = "1"

src/ArrayFuncs.jl

@@ -1,4 +1,4 @@
-import SeisIO: demean, demean!, taper, taper!,detrend, detrend!
+import SeisBase: demean, demean!, taper, taper!,detrend, detrend!
 export detrend, detrend!, taper, taper!, demean, demean!, hanningwindow
 # Signal processing functions for arrays (rather than SeisData or SeisChannel)
 

src/SeisNoise.jl

@@ -1,6 +1,6 @@
 module SeisNoise
 
-using Dates, DSP, FFTW, Glob, JLD2, LinearAlgebra, SeisIO, SeisIO.Nodal
+using Dates, DSP, FFTW, Glob, JLD2, LinearAlgebra, SeisBase, SeisBase.Nodal
 using Statistics, StatsBase, CUDA, Adapt, GPUArrays, RecipesBase
 
 # check use of cuda

src/Types/NoiseData.jl

@@ -1,10 +1,10 @@
 import Base: in, +, -, *, ==, convert, isempty, isequal, length, push!, sizeof, append!
 import Base: lastindex, firstindex, getindex, setindex!, sort, sort!
-import SeisIO: GeoLoc, PZResp, InstrumentResponse
+import SeisBase: GeoLoc, PZResp, InstrumentResponse
 export RawData, FFTData, CorrData, gpu, cpu, sort, sort!, append!
 export isequal, isempty, length, +, ==
 
-# Many thanks to SeisIO for inspiration for NoiseData objects
+# Many thanks to SeisBase for inspiration for NoiseData objects
 
 const datafields = (:x,:fft,:corr)
 
@@ -28,7 +28,7 @@ A structure for raw ambient noise data.
 | :cc_len     | Raw data window length in seconds. |
 | :cc_step    | Spacing between windows in seconds. |
 | :time_norm  | Apply one-bit whitening with "one_bit". |
-| :resp       | SeisIO InstrumentResponse object |
+| :resp       | SeisBase InstrumentResponse object |
 | :misc       | Dictionary for non-critical information. |
 | :notes      | Timestamped notes; includes automatically-logged acquisition and |
 |             | processing information. |
@@ -185,7 +185,7 @@ A structure for fourier transforms (FFT) of ambient noise data.
 | :cc_step    | Spacing between windows in number of points. |
 | :whitened   | Whitening applied.
 | :time_norm  | Apply one-bit whitening with "one_bit". |
-| :resp       | SeisIO InstrumentResponse object |
+| :resp       | SeisBase InstrumentResponse object |
 | :misc       | Dictionary for non-critical information. |
 | :notes      | Timestamped notes; includes automatically-logged acquisition and |
 |             | processing information. |
@@ -282,7 +282,7 @@ A structure for cross-correlations of ambient noise data.
 | :cc_step    | Spacing between windows in number of points. |
 | :whitened   | Whitening applied.
 | :time_norm  | Apply one-bit whitening with "one_bit". |
-| :resp       | SeisIO InstrumentResponse object |
+| :resp       | SeisBase InstrumentResponse object |
 | :misc       | Dictionary for non-critical information. |
 | :notes      | Timestamped notes; includes automatically-logged acquisition and |
 |             | processing information. |

src/Types/show.jl

@@ -26,19 +26,19 @@ function show(io::IO, R::RawData)
       fstr = uppercase(String(f))
       print(io, lpad(fstr, show_os-2), ": ")
       if f == :notes || f == :misc
-        SeisIO.show_str(io, String[string(length(targ), " entries")], w, N)
+        SeisBase.show_str(io, String[string(length(targ), " entries")], w, N)
       elseif (t <: AbstractFloat || t <: InstrumentPosition || t<: InstrumentResponse)
         println(io, repr("text/plain", targ, context=:compact=>true))
       elseif f == :t
         if length(R.t) > 0
-          SeisIO.show_str(io, String[timestamp(R.t[1]), " (", string(length(R.t)), " windows)"], w, N)
+          SeisBase.show_str(io, String[timestamp(R.t[1]), " (", string(length(R.t)), " windows)"], w, N)
         else
-          SeisIO.show_str(io, String[repr("text/plain", targ, context=:compact=>true)], w, N)
+          SeisBase.show_str(io, String[repr("text/plain", targ, context=:compact=>true)], w, N)
         end
       elseif f == :x
-        SeisIO.show_str(io, String[summary(targ)], w, N)
+        SeisBase.show_str(io, String[summary(targ)], w, N)
       else
-        SeisIO.show_str(io, String[repr("text/plain", targ, context=:compact=>true)], w, N)
+        SeisBase.show_str(io, String[repr("text/plain", targ, context=:compact=>true)], w, N)
       end
     end
   end
@@ -63,19 +63,19 @@ function show(io::IO, F::FFTData)
       fstr = uppercase(String(f))
       print(io, lpad(fstr, show_os-2), ": ")
       if f == :notes || f == :misc
-        SeisIO.show_str(io, String[string(length(targ), " entries")], w, N)
+        SeisBase.show_str(io, String[string(length(targ), " entries")], w, N)
       elseif (t <: AbstractFloat || t <: InstrumentPosition || t<: InstrumentResponse)
         println(io, repr("text/plain", targ, context=:compact=>true))
       elseif f == :t
         if length(F.t) > 0
-          SeisIO.show_str(io, String[timestamp(F.t[1]), " (", string(length(F.t)), " FFTs)"], w, N)
+          SeisBase.show_str(io, String[timestamp(F.t[1]), " (", string(length(F.t)), " FFTs)"], w, N)
         else
-          SeisIO.show_str(io, String[repr("text/plain", targ, context=:compact=>true)], w, N)
+          SeisBase.show_str(io, String[repr("text/plain", targ, context=:compact=>true)], w, N)
         end
       elseif f == :fft
-        SeisIO.show_str(io, String[summary(targ)], w, N)
+        SeisBase.show_str(io, String[summary(targ)], w, N)
       else
-        SeisIO.show_str(io, String[repr("text/plain", targ, context=:compact=>true)], w, N)
+        SeisBase.show_str(io, String[repr("text/plain", targ, context=:compact=>true)], w, N)
       end
     end
   end
@@ -99,19 +99,19 @@ function show(io::IO, C::CorrData)
       fstr = uppercase(String(f))
       print(io, lpad(fstr, show_os-2), ": ")
       if f == :notes || f == :misc
-        SeisIO.show_str(io, String[string(length(targ), " entries")], w, N)
+        SeisBase.show_str(io, String[string(length(targ), " entries")], w, N)
       elseif (t <: AbstractFloat || t <: InstrumentPosition || t<: InstrumentResponse)
         println(io, repr("text/plain", targ, context=:compact=>true))
       elseif f == :t
         if length(C.t) > 0
-          SeisIO.show_str(io, String[timestamp(C.t[1]), " (", string(length(C.t)), " Corrs)"], w, N)
+          SeisBase.show_str(io, String[timestamp(C.t[1]), " (", string(length(C.t)), " Corrs)"], w, N)
         else
-          SeisIO.show_str(io, String[repr("text/plain", targ, context=:compact=>true)], w, N)
+          SeisBase.show_str(io, String[repr("text/plain", targ, context=:compact=>true)], w, N)
         end
       elseif f == :corr
-        SeisIO.show_str(io, String[summary(targ)], w, N)
+        SeisBase.show_str(io, String[summary(targ)], w, N)
       else
-        SeisIO.show_str(io, String[repr("text/plain", targ, context=:compact=>true)], w, N)
+        SeisBase.show_str(io, String[repr("text/plain", targ, context=:compact=>true)], w, N)
       end
     end
   end

src/filter.jl

@@ -1,5 +1,5 @@
 import DSP: resample
-import SeisIO: resample, resample!
+import SeisBase: resample, resample!
 export bandpass, bandpass!, bandstop, bandstop!, lowpass, lowpass!
 export highpass, highpass!, taper, taper!, envelope
 export resample, resample!
@@ -409,23 +409,23 @@ end
 """
     resample!(R, fs)
 
-Resample data in `RawData` R to new sampling rate `fs`. 
+Resample data in `RawData` R to new sampling rate `fs`.
 
 # Arguments
-- `R::RawData`: RawData to resample. 
+- `R::RawData`: RawData to resample.
 - `fs::Real`: New sampling frequency.
 """
 function resample!(R::RawData,fs::Real)
     @assert fs > 0 "New fs must be greater than 0!"
     if R.fs == fs
-        return nothing 
+        return nothing
     end
     T = eltype(R.x)
     rate = T(fs / R.fs)
     R.x = resample_kernel(R.x, rate)
     R.fs = Float64(fs)
     if (R.freqmax <  fs / 2) && (rate < 1.0)
-        R.freqmax = Float64(fs / 2) 
+        R.freqmax = Float64(fs / 2)
     end
     return nothing
 end
@@ -434,30 +434,30 @@ resample(R::RawData,fs::Real) = (U = deepcopy(R); resample!(U,fs); return U)
 """
     resample!(C, fs)
 
-Resample data in CorrData` C to new sampling rate `fs`. 
+Resample data in CorrData` C to new sampling rate `fs`.
 
 # Arguments
-- `C::CorrData`: CorrData to resample. 
+- `C::CorrData`: CorrData to resample.
 - `fs::Real`: New sampling frequency.
 """
 function resample!(C::CorrData,fs::Real)
     @assert fs > 0 "New fs must be greater than 0!"
-    if C.fs == fs 
-        return nothing 
+    if C.fs == fs
+        return nothing
     end
     T = eltype(C.corr)
     rate = T(fs / C.fs)
     C.corr = resample_kernel(C.corr, rate)
     C.fs = Float64(fs)
     if (C.freqmax <  fs / 2) && (rate < 1.0)
-        C.freqmax = Float64(fs / 2) 
+        C.freqmax = Float64(fs / 2)
     end
     return nothing
 end
 resample(C::CorrData,fs::Real) = (U = deepcopy(C); resample!(U,fs); return U)
 
 function resample_kernel(x::AbstractMatrix,rate::Real)
-    T = eltype(x) 
+    T = eltype(x)
     h = resample_filter(rate)
     self = FIRFilter(h, rate)
 
@@ -469,7 +469,7 @@ function resample_kernel(x::AbstractMatrix,rate::Real)
     #   b) set the ϕ index of the PFB (fractional part of τ)
     setphase!(self, τ)
 
-    # calculate number of zeros 
+    # calculate number of zeros
     Nrows, Ncols = size(x)
     outLen = ceil(Int, Nrows*rate)
     reqInlen = inputlength(self, outLen)
@@ -485,4 +485,4 @@ function resample_kernel(x::AbstractMatrix,rate::Real)
         out[1:xlength,ii] .= filt(deepcopy(self), xPadded[:,ii])
     end
     return out
-end
+end

src/slicing.jl

@@ -1,4 +1,4 @@
-import SeisIO: sync
+import SeisBase: sync
 export start_end, slide, nearest_start_end, slide_ind, sync
 const μs = 1.0e-6
 const sμ = 1000000.0
@@ -9,7 +9,7 @@ const sμ = 1000000.0
 Return start and endtimes of SeisChannel in DateTime format.
 """
 function start_end(C::SeisChannel)
-    return u2d.(SeisIO.t_win(C.t,C.fs) * 1e-6)
+    return u2d.(SeisBase.t_win(C.t,C.fs) * 1e-6)
 end
 
 """
@@ -101,7 +101,7 @@ slide(C::SeisChannel, cc_len::Real, cc_step::Real) = slide(C.x,cc_len,cc_step,C.
 Return best possible start, end times for data in `C` given the `cc_step` and `cc_len`.
 """
 function nearest_start_end(C::SeisChannel, cc_len::Float64, cc_step::Float64)
-    su,eu = SeisIO.t_win(C.t,C.fs) * μs
+    su,eu = SeisBase.t_win(C.t,C.fs) * μs
     su = round(su,digits=4) # round due to numerical roundoff error
     eu = round(eu,digits=4) # round due to numerical roundoff error
     ideal_start = d2u(DateTime(Date(u2d(su)))) # midnight of same day

test/runtests.jl

@@ -1,11 +1,10 @@
-using Dates 
+using Dates
 using FFTW
 using Glob
-using SeisIO
+using SeisBase
 using SeisNoise
 using Statistics
 using Test
-import StatsBase: sample
 
 include("test_NoiseData.jl")
 include("test_show.jl")

test/test_correlation.jl

@@ -69,7 +69,7 @@ rand_id() = string(rand_net(), ".", rand_sta(), ".", rand_loc(), ".HH", rand('A'
     @test Cclean.freqmin == freqmin
     @test Cclean.freqmax == freqmax
     @test CInt.freqmin == freqmin
-    @test CInt.freqmax == freqmax 
+    @test CInt.freqmax == freqmax
 
     # test in-place
     clean_up!(C,freqmin,freqmax)
@@ -107,7 +107,7 @@ end
     @test all([t[maxinds[ii][1]] == 0 for ii in length(maxinds)])
 
     # test correlation with FFTData
-    Ch = SeisIO.RandSeis.randSeisChannel(c=false,s=true)
+    Ch = SeisBase.RandSeis.randSeisChannel(c=false,s=true)
     ungap!(Ch)
     Ch.x = rand(T,Int(cc_len*Nwin*fs +1)) .- T(0.5)
     Ch.fs = fs
@@ -125,7 +125,7 @@ end
     @test all([t[maxinds[ii][1]] == 0 for ii in length(maxinds)]) # test max args
     @test C.rotated == false # test rotation
     @test C.corr_type == "CC" # test cross-correlation
-    @test C.maxlag == CInt.maxlag 
+    @test C.maxlag == CInt.maxlag
     @test C.corr == CInt.corr
 
     # test windows that do not overlap
@@ -186,7 +186,7 @@ end
     Fhigh = whiten(F,freqmin,fs/2,fs,N,pad=pad)
     @test all(abs.(Fhigh[end-pad:end,:]) .< 1.)
 
-    # test with integer arguments 
+    # test with integer arguments
     FInt = whiten(F,Int(freqmin),Int(freqmax),Int(fs),N,pad=pad)
 
     # test in-place
@@ -195,7 +195,7 @@ end
     @test F == FInt
 
     # test FFTData
-    Ch = SeisIO.RandSeis.randSeisChannel(c=false,s=true)
+    Ch = SeisBase.RandSeis.randSeisChannel(c=false,s=true)
     Ch.loc = GeoLoc()
     ungap!(Ch)
     Ch.x = rand(T,Int(cc_len*Nwin*fs +1)) .- T(0.5)
@@ -230,7 +230,7 @@ end
     @test Fhigh.freqmin == freqmin
     @test Fhigh.freqmax == F.freqmax
 
-    # test with integer input 
+    # test with integer input
     FInt = whiten(F,Int(freqmin),Int(freqmax))
     @test FInt.freqmin == freqmin
     @test FInt.freqmax == freqmax
@@ -270,9 +270,9 @@ end
     @test Rhigh.freqmin == freqmin
     @test Rhigh.freqmax == R.freqmax
 
-    # test with integer input 
+    # test with integer input
     RInt = whiten(R,Int(freqmin),Int(freqmax))
-    @test RInt.freqmin == freqmin 
+    @test RInt.freqmin == freqmin
     @test RInt.freqmax == freqmax
 
     # test in-place

test/test_deprecated.jl

@@ -45,7 +45,7 @@ end
 @testset "compute cc" begin
     cc_len = 40.96 # length of noise window
     cc_step = 40.96 # step between windows
-    Ch = SeisIO.RandSeis.randSeisChannel(c=false,s=true)
+    Ch = SeisBase.RandSeis.randSeisChannel(c=false,s=true)
     ungap!(Ch)
     Ch.x = rand(T,Int(cc_len*Nwin*fs +1)) .- T(0.5)
     Ch.fs = fs

test/test_rotation.jl

@@ -13,7 +13,7 @@ starttime = d2u(DateTime(Date(now()))) # starttime for SeisChanel / SeisData
 
 @testset "rotation" begin
 
-    Ch = SeisIO.RandSeis.randSeisChannel(c=false,s=true)
+    Ch = SeisBase.RandSeis.randSeisChannel(c=false,s=true)
     ungap!(Ch)
     Ch.x = rand(T,Int(cc_len*Nwin*fs +1)) .- T(0.5)
     Ch.fs = fs