time stamps switched to microsec.

docs/src/seisdata.rst

@@ -149,4 +149,4 @@ Native File I/O
 ===============
 Use ``rseis`` and ``wseis`` to read and save in native format. Use ``writesac(S)`` to save trace data in ``S`` to single-channel :ref:`SAC <sac1>` files.
 
-SAC is widely used and well-supported, but writes in single-precision format. Rudimentary time stamping is enabled by default. Time stamped SAC data are treated by SAC itself as unevenly spaced, generic ``x-y`` data (``LEVEN=0, IFTYPE=4``). However, third-party SAC readers interpret such files less predictably: timestamped data *might* be loaded as the real part of a complex time series, with the time values themselves as the imaginary part...or the other way around...or not at all.
+The SAC file format is widely used and well-supported, but writes in single-precision format. Rudimentary time stamping is enabled by default. Time stamped SAC files from SeisIO are treated by the SAC program as unevenly spaced, generic ``x-y`` data (``LEVEN=0, IFTYPE=4``). However, third-party readers might interpret timestamped files less predictably: timestamped data *might* be loaded as the real part of a complex time series, with the time values stored as the imaginary part...or they might load the other way around...or they might not load at all.

docs/src/seisdata_fields.rst

@@ -53,7 +53,7 @@ Field Names and Meanings
 
 * ``notes``: array of notes
 
-* ``t``: pseudo-sparse two-column array of times
+* ``t``: pseudo-sparse two-column array of times :ref:`(see below) <seisdata_t>`
 
 * ``x``: vector of sample data
 
@@ -82,14 +82,16 @@ Scalars and single-type arrays of the follwoing types are OK: ``Char, Complex64,
 ---------
 The ``notes`` array grows automatically as data are modified. Any ``merge`` or ``sync`` operation is automatically noted. Additional notes can be written manually using the ``note`` command.
 
+.. _seisdata_t:
+
 ``t``
 -----
-For time series data (``fs > 0``), ``t`` is a sparse delta-encoded representation of *time gaps* in the correspoding data ``x``. The first column stores *indices*; the second column stores gap lengths in *seconds*.
+For *time series data* ``x``, ``t`` is a sparse delta-compressed representation of *time gaps in microseconds* in ``x``. The first column stores *indices*; the second column stores *gap lengths*.
 
-* The second column of the first row, i.e. ``t[1,2]``, always stores the time of the first sample in ``x`` relative to the Unix epoch (0.0 = 1970-01-01T00:00:00).
+* The second column of the first row, i.e. ``t[1,2]``, always stores the *time of the first sample* in ``x`` relative to the Unix epoch (e.g. ``t[1,2] = 10`` means the time series begins at 1970-01-01T00:00:00.000010 UTC).
 
 * The last row of ``t`` should always take the form ``[length(x) 0.0]``.
 
-* Other rows should take the form ``[(start of gap in x) (length of gap)]``.
+* Other rows should take the form ``[(starting index of gap in x) (length of gap)]``.
 
-For irregularly sampled data (``fs = 0``), ``t`` is a sparse delta-encoded representation of time stamps, one per sample. In this case, only the second column of ``t`` is used. The first column is usually a column of zeros.
+For *irregularly sampled data* (``fs = 0``), ``t`` is a dense delta-compressed representation of *time stamps in microseconds for each sample*. ``t`` for irregularly sampled data has a single column, but is treated by Julia as a two-dimensiona array (not a one-dimensional vector).

docs/src/seisdata_fileformat.rst

@@ -181,10 +181,10 @@ As with string arrays in ``misc``, split notes using the value of ``a`` as a cha
   :widths: 5, 32, 5, 5
 
   ``nt``, number of gaps, i64, 1
-  ``ti``, time gap indices, f64, ``nt``
-  ``tv``, time gap values, f64, ``nt``
+  ``ti``, time gap indices, i64, ``nt``
+  ``tv``, time gap values, i64, ``nt``
 
-``t`` is a two-column array, ``t = [ti tv]``.
+If ``fs>0, t`` is a two-column array, ``t = [ti tv]``; otherwise, Julia reshapes ``t`` to a one-column, two-dimensional array. 
 
 ``x``
 ^^^^^

src/FileFormats/LennartzAsc.jl

@@ -12,15 +12,15 @@ function rlennasc(fname::ASCIIString)
 
   sta = replace(h[3],"\'", "")
   S.fs = 1000/parse(h[5])
-  ts = Dates.datetime2unix(DateTime(join([h[8],"T",h[9]])))
+  ts = round(Int, Dates.datetime2unix(DateTime(join([h[8],"T",h[9]])))/μs)
 
   cmp = split(fname,'.')[end]
   x = readdlm(fid)
   close(fid)
 
   S.name = join([sta, cmp], '.')
   S.id = join(["", sta, "", cmp], '.')
-  S.t = map(Float64, [1.0 ts; length(S.x) 0.0])
+  S.t = [1 ts; length(S.x) 0]
   S.x = x[:,1]
   S.src = "lennartz ascii"
   return S

src/FileFormats/SAC.jl

@@ -280,7 +280,7 @@ function sactoseis(D::Dict{ASCIIString,Any})
     loc = [D["stla"], D["stlo"], D["stel"], 0, 0]
   end
   x = map(Float64, D["data"])
-  t = map(Float64, [1.0 sac2epoch(D); D["npts"] 0.0])
+  t = map(Float64, [1 sac2epoch(D)/μs; D["npts"] 0])
 
   misc = prunesac(D)
   for k in ["nvhdr", "knetwk", "kstnm", "kcmpnm", "scale",

src/FileFormats/SEGY.jl

@@ -337,7 +337,7 @@ function segytoseis(S::Dict{ASCIIString,Any})
     id = join(["",sta,"",cmp],'.')
   end
   x = S["data"]
-  t = map(Float64, [1.0 sac2epoch(S); length(x) 0])
+  t = [1 round(Int,sac2epoch(S)/μs); length(x) 0]
   gain = 1.0
   units = "unknown"
   loc = zeros(5)

src/FileFormats/UW.jl

@@ -457,7 +457,7 @@ function uwtoseis(S::Dict{ASCIIString,Any})
     src = S["src"]
     x = map(Float64, S["data"][i])
     notes = S["comment"]
-    t = map(Float64, [1.0 S["start"][i]+S["ot"]; length(x) 0])
+    t = [1 round(Int,(S["start"][i]+S["ot"])/μs); length(x) 0]
     misc = Dict{ASCIIString,Any}()
     for k in misc_keys
       misc[k] = S[k][i]

src/FileFormats/Win32.jl

@@ -221,7 +221,7 @@ function win32toseis(D = Dict{ASCIIString,Any}())
     # for an example of the (lack of) correspondence
 
     x = map(Float64, D[k]["data"].*D[k]["scale"])
-    t = [1.0 D[k]["startTime"]; length(D[k]["data"]) 0.0]
+    t = [1 round(Int,D[k]["startTime"]/μs); length(D[k]["data"]) 0]
     src = "win32"
     notes = [string(now, "  Record source: ", D[k]["netName"]);
              string(now, "  Location comment: ", D[k]["comment"]);

src/FileFormats/mSEED.jl

@@ -129,7 +129,7 @@ function parserec(S::SeisData, sid; v=false::Bool, vv=false::Bool, fmt=10::Int)
     # Lazy coding; I assume fs doesn't change
     channel = channel[1]
     dt = 1/S.fs[channel]
-    te = sum(S.t[channel][:,2]) + length(S.x[channel])*dt
+    te = sum(S.t[channel][:,2]) + length(S.x[channel])*round(Int,dt/μs)
   end
 
   # =========================================================================
@@ -213,13 +213,13 @@ function parserec(S::SeisData, sid; v=false::Bool, vv=false::Bool, fmt=10::Int)
   #te = ts + nsamp*dt
   vv && println("ts = ", ts, " te = ", te)
   if te  == 0
-    S.t[channel] = [1.0 ts; Float64(nsamp) 0.0]
+    S.t[channel] = [1 round(Int,ts/μs); nsamp 0]
   else
     S.t[channel] = S.t[channel][1:end-1,:]
     if ts-te > dt
-      S.t[channel] = [S.t[channel]; [length(S.x[channel])+1.0 ts-te]]
+      S.t[channel] = [S.t[channel]; [length(S.x[channel])+1 ts-te]]
     end
-    S.t[channel] = [S.t[channel]; [Float64(length(S.x[channel])+nsamp) 0.0]]
+    S.t[channel] = [S.t[channel]; [length(S.x[channel])+nsamp 0]]
   end
 
   # Data Read

src/SeisData/SeisData.jl

@@ -24,7 +24,7 @@ type SeisObj
   notes::Array{ASCIIString,1}
   resp::Array{Complex{Float64},2}
   src::ASCIIString
-  t::Array{Float64,2}
+  t::Array{Int64,2}
   x::Array{Float64,1}
   units::ASCIIString
 
@@ -37,7 +37,7 @@ type SeisObj
           notes=Array{ASCIIString,1}()::Array{ASCIIString,1},
           resp=Array{Complex{Float64},2}(0,2)::Array{Complex{Float64},2},
           src=""::ASCIIString,
-          t=Array{Float64,2}(0,2)::Array{Float64,2},
+          t=Array{Int64,2}(0,2)::Array{Int64,2},
           x=Array{Float64,1}()::Array{Float64,1},
           units=""::ASCIIString) = begin
      return new(name, id, fs, gain, loc, misc, notes, resp, src, t, x, units)
@@ -63,7 +63,7 @@ type SeisData
   notes::Array{Array{ASCIIString,1},1}         # notes
   resp::Array{Array{Complex{Float64},2},1}     # resp
   src::Array{ASCIIString,1}                    # src
-  t::Array{Array{Float64,2},1}                 # time
+  t::Array{Array{Int64,2},1}                 # time
   x::Array{Array{Float64,1},1}                 # data
   units::Array{ASCIIString,1}                  # units
 
@@ -78,7 +78,7 @@ type SeisData
     notes=Array{Array{ASCIIString,1},1}(),        # notes
     resp=Array{Array{Complex{Float64},2},1}(),    # resp
     src=Array{ASCIIString,1}(),                   # src
-    t=Array{Array{Float64,2},1}(),                # time
+    t=Array{Array{Int64,2},1}(),                # time
     x=Array{Array{Float64,1},1}(),                # data
     units=Array{ASCIIString,1}()                  # units
     ) = begin
@@ -275,70 +275,7 @@ delete!(S::SeisData, J::Array{Int,1}) = deleteat!(S, J)
 # ============================================================================
 # Merge and extract
 # Dealing with sparse time difference representations
-"""
-    t = t_expand(T::Array{Float64,2}, dt::Real)
-
-Expand sparse-difference (SeisData-style) time stamp representation t to full
-time stamps.
-"""
-function t_expand(t::Array{Float64,2}, dt::Real)
-  dt == Inf && return cumsum(t[:,2])
-  i = round(Int, t[:,1])
-  tt = dt.*ones(i[end])
-  tt[i] += t[:,2]
-  return cumsum(tt)
-end
-
-"""
-    t = t_collapse(T::Array{Float64,1}, dt::Real)
-
-Collapse full time stamp representation t to SeisData sparse-difference
-representation t.
-"""
-function t_collapse(t::Array{Float64,1}, dt::Real)
-  ts = map(Float32, [dt; diff(t)])
-  L = length(t)
-  i = find([!isapprox(ts[i],Float32(dt)) for i = 1:1:length(t)])
-  tt = cat(1, [1.0 t[1]], [map(Float64, i) ts[i]-dt])
-  (isempty(i) || i[length(i)] != Float64(L)) && (tt = cat(1, tt,
-    [Float64(L) 0.0]))
-  return tt
-end
 
-function xtmerge(t1::Array{Float64,2}, x1::Array{Float64,1},
-                 t2::Array{Float64,2}, x2::Array{Float64,1}, dt::Float64)
-  t = [t_expand(t1, dt); t_expand(t2, dt)]
-  if dt == Inf
-    dt = 0
-  end
-  x = [x1; x2]
-
-  # Sort
-  i = sortperm(t)
-  t1 = t[i]
-  x1 = x[i]
-
-  # Resolve conflicts
-  if minimum(diff(t1)) < 0.5*dt
-    J = flipdim(find(diff(t1) .< 0.5*dt), 1)
-    for j in J
-      t1[j] = 0.5*(t1[j]+t1[j+1])
-      if isnan(x1[j])
-        x1[j] = x1[j+1]
-      elseif !isnan(x1[j+1])
-        x1[j] = 0.5*(x1[j]+x1[j+1])
-      end
-      deleteat!(t1, j+1)
-      deleteat!(x1, j+1)
-    end
-  end
-  if 0 < dt < Inf
-    t1 = t_collapse(t1, dt)
-  else
-    t1 = [zeros(length(t1)) t1]
-  end
-  return (t1, x1)
-end
 
 """
     merge!(S::SeisObj, T::SeisObj)
@@ -361,7 +298,7 @@ function merge!(S::SeisObj, U::SeisObj)
   if !isapprox(S.gain,T.gain)
     (T.x .*= (S.gain/T.gain); T.gain = copy(S.gain))      # rescale T.x to match S.x
   end
-  (S.t, S.x) = xtmerge(S.t, S.x, T.t, T.x, 1/T.fs)        # merge time and data
+  (S.t, S.x) = xtmerge(S.t, S.x, T.t, T.x, T.fs)          # merge time and data
   merge!(S.misc, T.misc)                                  # merge misc
   S.notes = cat(1, S.notes, T.notes)                      # merge notes
   note(S, @sprintf("Merged %i samples", length(T.x)))
@@ -384,7 +321,7 @@ function merge!(S::SeisData, U::SeisObj)
   if !isapprox(S.gain[i],T.gain)
     (T.x .*= (S.gain[i]/T.gain); T.gain = copy(S.gain[i]))        # rescale T.x to match S.x
   end
-  (S.t[i], S.x[i]) = xtmerge(S.t[i], S.x[i], T.t, T.x, 1/T.fs)    # time, data
+  (S.t[i], S.x[i]) = xtmerge(S.t[i], S.x[i], T.t, T.x, T.fs)      # time, data
   merge!(S.misc[i], T.misc)                                       # misc
   S.notes[i] = cat(1, S.notes[i], T.notes)                        # notes
   note(S, i, @sprintf("Merged %i samples", length(T.x)))

src/SeisData/fileio.jl

@@ -37,7 +37,7 @@ function writesac(S::SeisData; ts=true, v=true)
     sacFloatVals[1] = Float32(dt)
     sacFloatVals[4] = Float32(S.gain[i])
     sacFloatVals[6] = Float32(0)
-    sacFloatVals[7] = Float32(dt*length(S.x[i]) + sum(S.t[i][2:end,2]))
+    sacFloatVals[7] = Float32(dt*length(S.x[i]) + sum(S.t[i][2:end,2])*μs)
     if !isempty(S.loc[i])
       sacFloatVals[32] = S.loc[i][1]
       sacFloatVals[33] = S.loc[i][2]
@@ -78,7 +78,7 @@ function writesac(S::SeisData; ts=true, v=true)
 
     # Data
     x = map(Float32, S.x[i])
-    ts && (tdata = map(Float32, t_expand(S.t[i], dt)-S.t[i][1,2]))
+    ts && (tdata = map(Float32, μs*(t_expand(S.t[i], dt)-S.t[i][1,2])))
 
     # Write to file
     sacwrite(fname, sacFloatVals, sacIntVals, sacCharVals, x, t=tdata, ts=ts)
@@ -388,11 +388,15 @@ function r_seisobj(io::IOStream)
   notes = read_string_array(io)
   T = read(io, Int64)
   if T > 0
-    ti = read(io, Float64, T)
-    tv = read(io, Float64, T)
-    t = [ti tv]
+    if fs > 0.0
+      ti = read(io, Int64, T)
+      tv = read(io, Int64, T)
+      t = [ti tv]
+    else
+      t = reshape(read(io, Int64, T), T, 1)
+    end
   else
-    t = Array{Float64,2}()
+    t = Array{Int64,2}()
   end
   X = read(io, Int64)
   if X > 0