From 6c08ab9bd5f383f4338896207d146d8597f2e437 Mon Sep 17 00:00:00 2001
From: Roger Herikstad <roger.herikstad@gmail.com>
Date: Thu, 15 Jun 2017 11:22:12 +0800
Subject: [PATCH] Adds new type for spike waveforms

---
 src/SpikeSorter.jl |  1 +
 src/io.jl          | 32 ++++++++++++++++++++++++++++++++
 src/types.jl       |  5 +++++
 test/io.jl         |  9 +++++++++
 test/runtests.jl   |  4 ++++
 5 files changed, 51 insertions(+)
 create mode 100644 src/io.jl
 create mode 100644 test/io.jl
 create mode 100644 test/runtests.jl

diff --git a/src/SpikeSorter.jl b/src/SpikeSorter.jl
index d53db78..1730f26 100644
--- a/src/SpikeSorter.jl
+++ b/src/SpikeSorter.jl
@@ -8,6 +8,7 @@ include("viterbi.jl")
 include("readfiles.jl")
 include("features.jl")
 include("extraction.jl")
+include("io.jl")
 import GUICheck
 if GUICheck.hasgui()
 	include("plot.jl")
diff --git a/src/io.jl b/src/io.jl
new file mode 100644
index 0000000..bb45ff2
--- /dev/null
+++ b/src/io.jl
@@ -0,0 +1,32 @@
+import Base.write
+
+function Base.write(io::IO, waveforms::SpikeWaveforms)
+    #write a header
+    headersize = 64
+    nbytes = 0
+    npoints, nchannels, nspikes = size(waveforms.waveforms) 
+    nbytes += write(io, npoints) 
+    nbytes += write(io, nchannels)
+    nbytes += write(io, nspikes)
+    seek(io, headersize)
+
+    #write timestamps, followed by waveforms
+    nbytes += write(io, waveforms.timestamps)
+    nbytes += write(io, waveforms.waveforms)
+    nbytes
+end
+
+function Base.read(io::IO, ::Type{SpikeWaveforms})
+    #read the header
+    headersize = 64
+    npoints = read(io, Int64)
+    nchannels = read(io, Int64)
+    nspikes = read(io, Int64)
+    seek(io, headersize)
+
+    #read timestamps
+    timestamps = read(io, Float64, nspikes)
+    waveforms = read(io, Float64, (npoints, nchannels, nspikes))
+    SpikeWaveforms(waveforms, timestamps)
+end
+
diff --git a/src/types.jl b/src/types.jl
index 3f29b17..0967c2e 100644
--- a/src/types.jl
+++ b/src/types.jl
@@ -1,5 +1,10 @@
 import HDF5
 
+type SpikeWaveforms
+    waveforms::Array{Float64,3}
+    timestamps::Array{Float64,1}
+end
+
 type TemplateFile
 	templates::Array{Float64,3}
 	cinv::Array{Float64,2}
diff --git a/test/io.jl b/test/io.jl
new file mode 100644
index 0000000..9fd41bd
--- /dev/null
+++ b/test/io.jl
@@ -0,0 +1,9 @@
+wf = SpikeSorter.SpikeWaveforms(randn(60,1,1024),cumsum(rand(1024)))
+fname = tempname()
+
+write(fname, wf)
+wf2 = read(fname, SpikeSorter.SpikeWaveforms)
+
+@test_approx_eq wf.timestamps wf2.timestamps
+@test_approx_eq wf.waveforms wf2.waveforms
+
diff --git a/test/runtests.jl b/test/runtests.jl
new file mode 100644
index 0000000..5639fd0
--- /dev/null
+++ b/test/runtests.jl
@@ -0,0 +1,4 @@
+using Base.Test
+using SpikeSorter
+
+include("io.jl")