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merge compat0.6 branch
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@sam81
sam81 committed Jul 30, 2017
2 parents bd5038c + 9db0b33 commit 7896d01
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Showing 3 changed files with 77 additions and 75 deletions.
3 changes: 2 additions & 1 deletion REQUIRE
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
Compat 0.7.18
DocStringExtensions
HDF5
julia 0.5
julia 0.6

138 changes: 69 additions & 69 deletions src/BDF.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ dats, evtTab, trigChan, sysChan = readBDF("res1.bdf", transposeData=true) #retur
function readBDF(fName::AbstractString; from::Real=0, to::Real=-1, channels::AbstractVector=[-1], transposeData::Bool=false)

channels = unique(channels)
if isa(channels, AbstractVector{Compat.ASCIIString})
if isa(channels, AbstractVector{String})
bdfHeader = readBDFHeader(fName)
channels = [findfirst(bdfHeader["chanLabels"], c) for c in channels]
channels = channels[channels .!= 0]
Expand All @@ -68,18 +68,18 @@ function readBDF(fid::IO; from::Real=0, to::Real=-1, channels::AbstractVector{In
nDataRecords = parse(Int, ascii(String(read(fid, UInt8, 8))))
recordDuration = float(ascii(String(read(fid, UInt8, 8))))
nChannels = parse(Int, ascii(String(read(fid, UInt8, 4))))
chanLabels = Array(Compat.ASCIIString, nChannels)
transducer = Array(Compat.ASCIIString, nChannels)
physDim = Array(Compat.ASCIIString, nChannels)
physMin = Array(Int32, nChannels)
physMax = Array(Int32, nChannels)
digMin = Array(Int32, nChannels)
digMax = Array(Int32, nChannels)
prefilt = Array(Compat.ASCIIString, nChannels)
nSampRec = Array(Int, nChannels)
reserved = Array(Compat.ASCIIString, nChannels)
scaleFactor = Array(Float32, nChannels)
sampRate = Array(Int, nChannels)
chanLabels = Array{String}(nChannels)
transducer = Array{String}(nChannels)
physDim = Array{String}(nChannels)
physMin = Array{Int32}(nChannels)
physMax = Array{Int32}(nChannels)
digMin = Array{Int32}(nChannels)
digMax = Array{Int32}(nChannels)
prefilt = Array{String}(nChannels)
nSampRec = Array{Int}(nChannels)
reserved = Array{String}(nChannels)
scaleFactor = Array{Float32}(nChannels)
sampRate = Array{Int}(nChannels)

duration = recordDuration*nDataRecords

Expand Down Expand Up @@ -143,12 +143,12 @@ function readBDF(fid::IO; from::Real=0, to::Real=-1, channels::AbstractVector{In
end
recordsToRead = to - from
if transposeData
data = Array(Int32, ((recordsToRead*nSampRec[1]), (nKeepChannels)))
data = Array{Int32}((recordsToRead*nSampRec[1]), (nKeepChannels))
else
data = Array(Int32, ((nKeepChannels), (recordsToRead*nSampRec[1])))
data = Array{Int32}((nKeepChannels), (recordsToRead*nSampRec[1]))
end
trigChan = Array(Int16, recordsToRead*nSampRec[1])
sysCodeChan = Array(Int16, recordsToRead*nSampRec[1])
trigChan = Array{Int16}(recordsToRead*nSampRec[1])
sysCodeChan = Array{Int16}(recordsToRead*nSampRec[1])

startPos = 3*from*nChannels*nSampRec[1]
skip(fid, startPos)
Expand Down Expand Up @@ -221,7 +221,7 @@ function readBDF(fid::IO; from::Real=0, to::Real=-1, channels::AbstractVector{In
trigDurs = (stopPoints - startPoints)/sampRate[1]

evt = trigChan[startPoints]
evtTab = @compat Dict{Compat.ASCIIString,Any}("code" => evt,
evtTab = Dict{String,Any}("code" => evt,
"idx" => startPoints,
"dur" => trigDurs
)
Expand Down Expand Up @@ -297,18 +297,18 @@ function readBDFHeader(fid::IO; fName::AbstractString="")
nDataRecords = parse(Int, ascii(String(read(fid, UInt8, 8))))
recordDuration = float(ascii(String(read(fid, UInt8, 8))))
nChannels = parse(Int, ascii(String(read(fid, UInt8, 4))))
chanLabels = Array(Compat.ASCIIString, nChannels)
transducer = Array(Compat.ASCIIString, nChannels)
physDim = Array(Compat.ASCIIString, nChannels)
physMin = Array(Int32, nChannels)
physMax = Array(Int32, nChannels)
digMin = Array(Int32, nChannels)
digMax = Array(Int32, nChannels)
prefilt = Array(Compat.ASCIIString, nChannels)
nSampRec = Array(Int, nChannels)
reserved = Array(Compat.ASCIIString, nChannels)
scaleFactor = Array(Float32, nChannels)
sampRate = Array(Int, nChannels)
chanLabels = Array{String}(nChannels)
transducer = Array{String}(nChannels)
physDim = Array{String}(nChannels)
physMin = Array{Int32}(nChannels)
physMax = Array{Int32}(nChannels)
digMin = Array{Int32}(nChannels)
digMax = Array{Int32}(nChannels)
prefilt = Array{String}(nChannels)
nSampRec = Array{Int}(nChannels)
reserved = Array{String}(nChannels)
scaleFactor = Array{Float32}(nChannels)
sampRate = Array{Int}(nChannels)

duration = recordDuration*nDataRecords

Expand Down Expand Up @@ -359,32 +359,32 @@ function readBDFHeader(fid::IO; fName::AbstractString="")

close(fid)

d = @compat Dict{Compat.ASCIIString,Any}("fileName" => fName,
"idCodeNonASCII" => idCodeNonASCII,
"idCode" => idCode,
"subjID" => subjID,
"recID" => recID,
"startDate" => startDate,
"startTime" => startTime,
"nBytes" => nBytes,
"versionDataFormat" => versionDataFormat,
"nDataRecords" => nDataRecords,
"recordDuration" => recordDuration,
"nChannels" => nChannels,
"chanLabels" => chanLabels,
"transducer" => transducer,
"physDim"=> physDim,
"physMin" => physMin,
"physMax" => physMax,
"digMin" => digMin,
"digMax" => digMax,
"prefilt" => prefilt,
"nSampRec" => nSampRec,
"reserved" => reserved,
"scaleFactor" => scaleFactor,
"sampRate" => sampRate,
"duration" => duration,
)
d = Dict{String,Any}("fileName" => fName,
"idCodeNonASCII" => idCodeNonASCII,
"idCode" => idCode,
"subjID" => subjID,
"recID" => recID,
"startDate" => startDate,
"startTime" => startTime,
"nBytes" => nBytes,
"versionDataFormat" => versionDataFormat,
"nDataRecords" => nDataRecords,
"recordDuration" => recordDuration,
"nChannels" => nChannels,
"chanLabels" => chanLabels,
"transducer" => transducer,
"physDim"=> physDim,
"physMin" => physMin,
"physMax" => physMax,
"digMin" => digMin,
"digMax" => digMax,
"prefilt" => prefilt,
"nSampRec" => nSampRec,
"reserved" => reserved,
"scaleFactor" => scaleFactor,
"sampRate" => sampRate,
"duration" => duration,
)
return(d)

end
Expand Down Expand Up @@ -436,8 +436,8 @@ writeBDF("bdfRec.bdf", dats, trigs, statChan, sampRate, startDate="23.06.14",
startTime="10.18.19")
```
"""
function writeBDF{P<:Real, Q<:Real, R<:Real, S<:Compat.ASCIIString, T<:Compat.ASCIIString, U<:Compat.ASCIIString, V<:Real, W<:Real, Z<:Compat.ASCIIString}(fName::AbstractString, data::AbstractMatrix{P}, trigChan::AbstractVector{Q}, statusChan::AbstractVector{R}, sampRate::Integer; subjID::Compat.ASCIIString="",
recID::Compat.ASCIIString="", startDate::Compat.ASCIIString=Libc.strftime("%d.%m.%y", time()), startTime::Compat.ASCIIString=Libc.strftime("%H.%M.%S", time()), versionDataFormat::Compat.ASCIIString="24BIT",
function writeBDF{P<:Real, Q<:Real, R<:Real, S<:String, T<:String, U<:String, V<:Real, W<:Real, Z<:String}(fName::AbstractString, data::AbstractMatrix{P}, trigChan::AbstractVector{Q}, statusChan::AbstractVector{R}, sampRate::Integer; subjID::String="",
recID::String="", startDate::String=Libc.strftime("%d.%m.%y", time()), startTime::String=Libc.strftime("%H.%M.%S", time()), versionDataFormat::String="24BIT",
chanLabels::AbstractVector{S}=["" for i=1:size(data)[1]],
transducer::AbstractVector{T}=["" for i=1:size(data)[1]],
physDim::AbstractVector{U}=["" for i=1:size(data)[1]],
Expand Down Expand Up @@ -753,9 +753,9 @@ function writeBDF{P<:Real, Q<:Real, R<:Real, S<:Compat.ASCIIString, T<:Compat.AS
dats[i,:] = dats[i,:] /scaleFactor[i]
end

dats = round(Int32, dats) #need to pad dats
trigs = round(Int16, trigs)
statChan = round(Int16, statChan)
dats = round.(Int32, dats) #need to pad dats
trigs = round.(Int16, trigs)
statChan = round.(Int16, statChan)
for n=1:nDataRecords
for c=1:nChannels
if c < nChannels
Expand Down Expand Up @@ -809,7 +809,7 @@ function splitBDFAtTrigger(fName::AbstractString, trigger::Integer; from::Real=0
stopPoints = [sepPoints; size(data)[2]]

startDateTime = DateTime(string(origHeader["startDate"], ".", origHeader["startTime"]), "dd.mm.yy.HH.MM.SS")
timeSeconds = [0; round(Int, sepPoints.*sampRate)]
timeSeconds = [0; round.(Int, sepPoints.*sampRate)]

for i=1:nChunks
thisFname = joinpath(dirname(fName), basename(fName)[1:end-4] * "_" * string(i) * basename(fName)[end-3:end])
Expand Down Expand Up @@ -858,7 +858,7 @@ function splitBDFAtTime{T<:Real}(fName::AbstractString, timeSeconds::Union{T, Ab
data, evtTab, trigChan, sysCodeChan = readBDF(fName, from=from, to=to)
origHeader = readBDFHeader(fName)
sampRate = origHeader["sampRate"][1] #assuming sampling rate is the same for all channels
sepPoints = round(Int, sampRate.*timeSeconds)
sepPoints = round.(Int, sampRate.*timeSeconds)
for i=1:length(sepPoints)
if sepPoints[i] > size(data)[2]
error("Split point exceeds data points")
Expand Down Expand Up @@ -926,11 +926,11 @@ end
function decodeStatusChannel(statusChannel::AbstractVector{Int16})

n = length(statusChannel)
newEpoch = Array(Bool, n)
speedMode = Array(Int8, n)
CMSInRange = Array(Bool, n)
batteryLow = Array(Bool, n)
isMK2 = Array(Bool, n)
newEpoch = Array{Bool}(n)
speedMode = Array{Int8}(n)
CMSInRange = Array{Bool}(n)
batteryLow = Array{Bool}(n)
isMK2 = Array{Bool}(n)
for i=1:n
x = bin(statusChannel[i])
newEpoch[i] = parse(Bool, x[8])
Expand All @@ -940,7 +940,7 @@ function decodeStatusChannel(statusChannel::AbstractVector{Int16})
isMK2[i] = parse(Bool, x[1])
end

decodedStatusChannel = @compat Dict{Compat.ASCIIString,Any}("newEpoch" => newEpoch,
decodedStatusChannel = Dict{String,Any}("newEpoch" => newEpoch,
"speedMode" => speedMode,
"CMSInRange" => CMSInRange,
"batteryLow" => batteryLow,
Expand Down
11 changes: 6 additions & 5 deletions test/test_channel_select.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,15 +17,16 @@ for ci in ([1, 2, 3], [1, 2, 3, 4, 5, 6], 1:14, [1, 3, 9, 11, 15], [5, 2, 7])

end

for (ci, el) in zip((["A1", "A2"], ["A1", "A3"], ["A3", "A1", "A11", "A16"]), ([1, 2], [1, 3], [3, 1, 11, 16]))
for (chanLabs, chanNum) in zip((["A1", "A2"], ["A1", "A3"], ["A3", "A1", "A11", "A16"]), ([1, 2], [1, 3], [3, 1, 11, 16]))

dats2, evtTab2, trigs2, statusChan2 = readBDF(origFilePath, channels = ci)
dats2, evtTab2, trigs2, statusChan2 = readBDF(origFilePath, channels = chanLabs)

@test size(dats2, 2) == size(dats, 2)
@test size(dats2, 1) == length(ci)
@test size(dats2, 1) == length(chanLabs)

#@test_approx_eq(dats[el, :], dats2)
#@test_approx_eq(dats[el[1], 1], dats2[1,1])
@test isequal(dats[el, :], dats2)
#@test dats[el, :] ≈ dats2
@test isequal(dats[chanNum, :], dats2)

@test statusChan2 == statusChan
end

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