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Test MNE can read our exports #71

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1ede0f1
test we can load EDFs into MNE
ericphanson Oct 16, 2023
85bcd38
format
ericphanson Oct 16, 2023
1c43bee
undo formatting changes
ericphanson Oct 16, 2023
22851be
restore trailing whitespace
ericphanson Oct 16, 2023
5654070
fix tests
ericphanson Oct 16, 2023
ae560b3
simpler test
ericphanson Oct 16, 2023
fa72af4
Merge remote-tracking branch 'origin/main' into eph/mne-tests
kleinschmidt Mar 20, 2024
e06d13f
Fix formatting
ararslan Apr 5, 2024
b62e8f8
Merge branch 'main' into eph/mne-tests
ericphanson Oct 8, 2024
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1 change: 1 addition & 0 deletions .JuliaFormatter.toml
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
style = "yas"
2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -12,7 +12,7 @@ jobs:
fail-fast: false
matrix:
version:
- '1.4' # Earliest supported version
- '1.6' # Earliest supported version
- '1' # Latest release
- 'nightly'
os:
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8 changes: 6 additions & 2 deletions Project.toml
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Expand Up @@ -9,13 +9,17 @@ Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"

[compat]
Accessors = "0.1"
BitIntegers = "0.2"
FilePathsBase = "0.9.13"
julia = "1.4"
PyMNE = "0.2.2"
julia = "1.6"

[extras]
Accessors = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
FilePathsBase = "48062228-2e41-5def-b9a4-89aafe57970f"
PyMNE = "6c5003b2-cbe8-491c-a0d1-70088e6a0fd6"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[targets]
test = ["FilePathsBase", "Test"]
test = ["Accessors", "FilePathsBase", "PyMNE", "Test"]
32 changes: 31 additions & 1 deletion test/runtests.jl
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Expand Up @@ -4,6 +4,8 @@ using EDF: TimestampedAnnotationList, PatientID, RecordingID, SignalHeader,
using Dates
using FilePathsBase
using Test
using PyMNE
using Accessors

#####
##### Testing utilities
Expand Down Expand Up @@ -33,6 +35,17 @@ end

deep_equal(a::T, b::S) where {T,S} = false

function mne_read(edf)
tmpfile = joinpath(mktempdir(), "test.edf")
EDF.write(tmpfile, edf)
# Check we can load it and do something with it
py = PyMNE.io.read_raw_edf(tmpfile; verbose=false)
py.load_data(; verbose=false)
data = pyconvert(Array, py.get_data())
@test data isa Matrix
return py
end

#####
##### Actual tests
#####
Expand Down Expand Up @@ -93,6 +106,14 @@ const DATADIR = joinpath(@__DIR__, "data")
EDF.read!(file)
@test deep_equal(edf.signals, file.signals)

# Check we can read it into MNE
py = mne_read(edf)
@test length(py.annotations) == 5
ann = py.annotations[1]
@test pyconvert(Float64, ann["onset"]) == 0.1344
@test pyconvert(Float64, ann["duration"]) == 0.256
@test pyconvert(String, ann["description"]) == "type A"

# test that EDF.write(::IO, ::EDF.File) errors if file is
# discontiguous w/o an AnnotationsSignal present
bad_file = EDF.File(IOBuffer(),
Expand Down Expand Up @@ -182,7 +203,7 @@ const DATADIR = joinpath(@__DIR__, "data")
@test_logs((:warn,
"Number of data records in file header does not match " *
"file size. Skipping 1 truncated data record(s)."),
EDF.read(truncated_file))
EDF.read(truncated_file))
edf = EDF.read(joinpath(DATADIR, full_file))
truncated_edf = EDF.read(truncated_file)
for field in fieldnames(EDF.FileHeader)
Expand Down Expand Up @@ -253,6 +274,15 @@ const DATADIR = joinpath(@__DIR__, "data")
edf = EDF.File(io)
@test sprint(show, edf) == "EDF.File with 140 16-bit-encoded signals"
end

@testset "Exports readable by MNE" begin
edf = EDF.read(joinpath(DATADIR, "test_float_extrema.edf"))
@test edf.signals[1].header.digital_minimum ≈ -32767.0f0
edf = @set edf.signals[1].header.digital_minimum = -32767 * 2
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I don't understand what the purpose of this is. If it's necessary for testing a particular behavior, can you add a comment? I think it's the only use of Accessors here so if it's not actually necessary then dropping it would reduce the number of test dependencies.

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this PR was meant to complement #72 which uses Accessors more extensively in the tests

however I no longer remember what the point of this line is anymore :/


py = mne_read(edf)
@test isempty(py.annotations)
end
end

@testset "BDF+ Files" begin
Expand Down