Add docs

.gitignore

@@ -0,0 +1,24 @@
+# Files generated by invoking Julia with --code-coverage
+*.jl.cov
+*.jl.*.cov
+
+# Files generated by invoking Julia with --track-allocation
+*.jl.mem
+
+# System-specific files and directories generated by the BinaryProvider and BinDeps packages
+# They contain absolute paths specific to the host computer, and so should not be committed
+deps/deps.jl
+deps/build.log
+deps/downloads/
+deps/usr/
+deps/src/
+
+# Build artifacts for creating documentation generated by the Documenter package
+docs/build/
+docs/site/
+
+# File generated by Pkg, the package manager, based on a corresponding Project.toml
+# It records a fixed state of all packages used by the project. As such, it should not be
+# committed for packages, but should be committed for applications that require a static
+# environment.
+Manifest.toml

docs/make.jl

@@ -0,0 +1,29 @@
+push!(LOAD_PATH,"../src/")
+using Documenter, Noise
+
+makedocs(
+ modules = [Noise],
+ format = Documenter.HTML(),
+ sitename = "Noise.jl",
+ authors = "Tim Clements",
+ pages = Any[
+ "Home" => "index.md",
+ "Pre-Processing" => "preprocessing.md",
+ "Array Functions" => "arrayfuncs.md",
+ "Filters" => "filter.md",
+ "Computing FFTs" => "fft.md",
+ "Correlation" => "correlation.md",
+ "Types" => Any[
+ "InputParams" => "Types/inputparams.md",
+ "FFTData" => "Types/fftdata.md",
+ "CorrData" => "Types/corrdata.md",
+ ],
+ ],
+)
+
+deploydocs(
+ repo = "github.com/tclements/Noise.jl.git",
+ target = "build",
+ deps = nothing,
+ make = nothing,
+)

docs/src/Types/corrdata.md

@@ -0,0 +1,5 @@
+`CorrData` - Objects for ambient noise cross-correlations.
+
+```@docs
+CorrData
+```

docs/src/Types/fftdata.md

@@ -0,0 +1,5 @@
+`FFTData` - Objects for holding Fourier transforms (FFTs)
+
+```@docs
+FFTData
+```

docs/src/Types/inputparams.md

@@ -0,0 +1,5 @@
+`Input Parameters` - Objects for scheduling cross-correlations
+
+```@docs
+InputParams
+```

docs/src/arrayfuncs.md

@@ -0,0 +1,6 @@
+# `Array Functions` - methods for operating on array-based noise and corelations.
+
+```@docs
+detrend!
+demean!
+```

docs/src/correlation.md

@@ -0,0 +1,10 @@
+# `Computing Correlations` - methods for computing correlations from FFTs.
+
+```@docs
+clean_up!
+correlate
+compute_cc
+next_fast_len
+save_corr
+load_fft
+```

docs/src/fft.md

@@ -0,0 +1,7 @@
+# `Computing FFTs` - methods for computing FFTs raw noise data.
+
+```@docs
+whiten
+process_fft
+save_fft
+```

docs/src/filter.md

@@ -0,0 +1,8 @@
+# `Filters` - methods for filtering `SeisData` and `SeisChannel` objects.
+
+```@docs
+bandpass!
+bandstop!
+lowpass!
+highpass!
+```

docs/src/index.md

@@ -0,0 +1,20 @@
+# Noise.jl
+
+*Ambient Noise Cross-Correlation in Julia.*
+
+Noise.jl provides routines for quickly and efficiently implementing [seismic interferometry](https://en.wikipedia.org/wiki/Seismic_interferometry).
+
+## Package Features
+ - Built upon [SeisIO](https://seisio.readthedocs.io/en/latest/) for easy and fast I/O.
+ - Custom types for saving Fourier Transforms of data and cross-correlations
+ - Array-based processing of raw data and cross-correlation.
+ - Coming soon: methods for $dv/v$ and dispersion measurements.
+ - Coming soon: GPU support.
+
+## Processing
+
+## Plotting
+
+## High-Performance Computing
+
+## Tutorial

docs/src/preprocessing.md

@@ -0,0 +1,9 @@
+# `Pre-Processing` - methods for cleaning raw noise data.
+
+```@docs
+process_raw!
+downsample
+slide
+start_end
+nearest_start_end
+```

src/ArrayFuncs.jl

@@ -1,5 +1,5 @@
 export detrend, detrend!, demean, demean!, bandpass, bandpass!, bandstop, bandstop!,
- lowpass, lowpass!, highpass, highpass! 
+ lowpass, lowpass!, highpass, highpass!
 import Statistics.mean
 import LinearAlgebra.pinv
 using DSP
@@ -22,9 +22,9 @@ function lstsq(A::AbstractArray,X::AbstractArray)
 end
 
 """
- detrend!(A)
+ detrend!(X::AbstractArray{<:Union{Float32,Float64},1})
 
-Remove linear trend from array `A` using least-squares regression.
+Remove linear trend from array `X` using least-squares regression.
 """
 function detrend!(X::AbstractArray{<:Union{Float32,Float64},1})
  N = length(X)
@@ -38,7 +38,7 @@ detrend(A::AbstractArray{<:Union{Float32,Float64},1}) = (U = deepcopy(A);
  detrend!(U);return U)
 
 """
- detrend!(A)
+ detrend!(X::AbstractArray{<:Union{Float32,Float64},2})
 
 Remove linear trend from columns of `X` using least-squares regression.
 """
@@ -56,7 +56,7 @@ detrend(A::AbstractArray{<:Union{Float32,Float64},2}) = (U = deepcopy(A);
  detrend!(U);return U)
 
 """
- demean!(A)
+ demean!(A::AbstractArray{<:Union{Float32,Float64},1})
 
 Remove mean from array `A`.
 """
@@ -71,7 +71,7 @@ demean(A::AbstractArray{<:Union{Float32,Float64},1}) = (U = deepcopy(A);
  demean!(U);return U)
 
 """
- demean!(A)
+ demean!(A::AbstractArray{<:Union{Float32,Float64},2})
 
 Remove mean from columns of array `A`.
 """

src/Types/CorrData.jl

@@ -5,7 +5,33 @@ const corrfields = [:id, :name, :loc, :comp, :rotated, :corr_type, :fs, :gain,
  :freqmin, :freqmax, :cc_step, :whitened, :time_norm, :resp,
  :notes, :misc, :maxlag, :t, :corr]
 
-# This is type-stable for C = CorrData() but not for keyword args
+"""
+ CorrData
+
+A structure for cross-correlations of ambient noise data.
+
+## Fields: CorrData
+| **Field** | **Description** |
+|:------------|:-------------|
+| :name | Freeform channel names |
+| :id | Channel ids. use NET.STA.LOC.CHAN format when possible. |
+| :loc | Location (position) vector; freeform. |
+| :fs | Sampling frequency in Hz. |
+| :gain | Scalar gain; divide data by the gain to convert to units |
+| :freqmin | Minimum frequency for whitening. |
+| :freqmax | Maximum frequency for whitening. |
+| :cc_len | Length of each correlation in seconds. |
+| :cc_step | Spacing between correlation windows in seconds. |
+| :whitened | Whitening applied.
+| :time_norm | Apply one-bit whitening with "one_bit". |
+| :resp | Instrument response; two-column matrix, format [zeros poles] |
+| :misc | Dictionary for non-critical information. |
+| :notes | Timestamped notes; includes automatically-logged acquisition and |
+| | processing information. |
+| :maxlag | Maximum lag time in seconds to keep from correlations. |
+| :t | Starttime of each correlation. |
+| :corr | Correlations stored in columns. |
+"""
 mutable struct CorrData
  name::String # name [Net1.Sta1.Loc1.Chan1.Net2.Sta2.Loc2.Chan2]
  id::String # id [Y-mm-dd] this is date of corr

src/Types/FFTData.jl

@@ -4,7 +4,33 @@ export FFTData
 const fftfields = [:id, :name, :loc, :fs, :gain, :freqmin, :freqmax, :cc_step,
  :whitened, :time_norm, :resp,:notes, :misc, :t, :fft]
 
-# This is type-stable for F = FFTData() but not for keyword args
+"""
+ FFTData
+
+A structure for fourier transforms (FFT) of ambient noise data.
+
+## Fields: FFTData
+| **Field** | **Description** |
+|:--------------------|:--------------------|
+| :name | Freeform channel names |
+| :id | Channel ids. use NET.STA.LOC.CHAN format when possible. |
+| :loc | Location (position) vector; freeform. |
+| :fs | Sampling frequency in Hz. |
+| :gain | Scalar gain; divide data by the gain to convert to units |
+| :freqmin | Minimum frequency for whitening. |
+| :freqmax | Maximum frequency for whitening. |
+| :cc_len | Length of each correlation in seconds. |
+| :cc_step | Spacing between correlation windows in seconds. |
+| :whitened | Whitening applied.
+| :time_norm | Apply one-bit whitening with "one_bit". |
+| :resp | Instrument response; two-column matrix, format [zeros poles] |
+| :misc | Dictionary for non-critical information. |
+| :notes | Timestamped notes; includes automatically-logged acquisition and |
+| | processing information. |
+| :maxlag | Maximum lag time in seconds to keep from correlations. |
+| :t | Starttime of each FFT. |
+| :fft | FFTs stored in columns. |
+"""
 mutable struct FFTData
  name::String # name [Net.Sta.Loc.Chan]
  id::String # id [Y-mm-dd] this is date of fft

src/Types/InputParams.jl

@@ -1,5 +1,27 @@
 export InputParams
 
+"""
+ InputParams
+
+A structure for inputing parameters necessary for processing ambient noise data.
+
+## Fields: InputParams
+| **Field** | **Description** |
+|:--------------------|:--------------------|
+| :pair | Network.Station.Channel for each station to be correlated. |
+| :FFTOUT | Directory filepath for FFT output. |
+| :CORROUT | Directory filepath for correlation output. |
+| :cc_len | Length of each correlation in seconds. |
+| :cc_step | Spacing between correlation windows in seconds. |
+| :fs | Sampling frequency in Hz to downsample raw data; set to 0.0. |
+| :freqmin | Minimum frequency for whitening. |
+| :freqmax | Maximum frequency for whitening. |
+| :time_norm | Apply one-bit whitening with "one_bit". |
+| :to_whiten | Apply whitening to FFTs. |
+| :maxlag | Maximum lag time in seconds to keep from correlations. |
+| :smoothing_half_win | Half window in samples for FFT smoothing. |
+| :corr_type | Type of correlation e.g. "cross-correlate", "deconv" or "coherence" |
+"""
 mutable struct InputParams
  pair::Array{String,1}
  FFTOUT::String

src/downsample.jl

@@ -35,7 +35,7 @@ function downsample(C::SeisChannel,fs::Float64)
 end
 
 """
- downsample(S::SeisData)
+ downsample(S::SeisData, fs::Float64)
 
 Downsample SeisData sampling rate to frequency `fs`.
 """