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beacon-biosignals / EDF.jl

Read and write EDF files in Julia
MIT License
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EDF.jl does not allow truncating header values to 0, even when it should #74

Open ericphanson opened 12 months ago

ericphanson commented 12 months ago

Here I use OndaEDF to more easily construct the EDF.File object, but I believe the bug is in EDF.write.

Setup:

using OndaEDF, Onda, EDF
info = SamplesInfoV2(; sensor_type="x",
    channels=["x"],
    sample_unit="microvolt",
    sample_resolution_in_unit=1,
    sample_offset_in_unit=0,
    sample_type=Float64,
    sample_rate=1)

data = reshape([1e-9, 1], 1,:)
samples = Samples(data, info, false)
edf = onda_to_edf([samples])

The resulting EDF looks like:

julia> edf.header
EDF.FileHeader("0", EDF.PatientID(missing, missing, missing, missing), EDF.RecordingID(missing, missing, missing, missing), DateTime("1985-01-01T00:00:00"), true, 2, 1.0)

julia> edf.signals
1-element Vector{Union{EDF.AnnotationsSignal, EDF.Signal{Int16}}}:
 EDF.Signal{Int16}(EDF.SignalHeader("X X", "", "uV", 1.0f-9, 1.0f0, -32768.0f0, 32767.0f0, "", 1), Int16[-32768, 32767])

julia> edf.signals[1].header.physical_minimum
1.0f-9

When we try to write it:

julia> EDF.write( IOBuffer(), edf)
ERROR: failed to fit number into EDF's 8 ASCII character limit: 1.0e-9
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:35
 [2] _edf_repr(x::Float32)
   @ EDF ~/EDF.jl/src/write.jl:37
 [3] edf_write(io::IOBuffer, value::Float32, byte_limit::Int64)
   @ EDF ~/EDF.jl/src/write.jl:49
 [4] write_header(io::IOBuffer, file::EDF.File{Int16, IOBuffer})
   @ EDF ~/EDF.jl/src/write.jl:95
 [5] write(io::IOBuffer, file::EDF.File{Int16, IOBuffer})
   @ EDF ~/EDF.jl/src/write.jl:180
 [6] top-level scope
   @ REPL[118]:1

The issue: EDF.jl does not want to round the physical_minimum down to zero, although that would be perfectly fine.

I think it is odd that the current _edf_repr code allows truncation to any value except 0, and if we have semantic concerns about truncating to 0, that should be checked in the EDF.File (or Signal) constructors on the appropriate fields, rather than applying to all numeric fields in _edf_repr.