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Update URLs in tests #36

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merged 4 commits into from
Oct 14, 2019
Merged

Update URLs in tests #36

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3e187e2
Update data url in tests. Replace gunzip with gzip.
notZaki Sep 6, 2019
ca713d3
Remove Julia v0.7 from tests. Add v1.2
notZaki Sep 6, 2019
46aa179
Replace dropbox with github URLs & remove gzip in tests
notZaki Sep 15, 2019
766c594
Refactor tests
notZaki Sep 15, 2019
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2 changes: 1 addition & 1 deletion .travis.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@ os:
- linux
- osx
julia:
- 0.7
- 1.0
- 1.2
- nightly
notifications:
email: false
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196 changes: 90 additions & 106 deletions test/runtests.jl
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Original file line number Diff line number Diff line change
@@ -1,39 +1,44 @@
using Test
using DICOM

testdir = joinpath(@__DIR__,"testdata")
if !isdir(testdir)
mkdir(testdir)
const data_folder = joinpath(@__DIR__,"testdata")
if !isdir(data_folder)
mkdir(data_folder)
end

# TEST SET 1: Simple Reading/Writing

fileMR = joinpath(testdir, "MR_Implicit_Little")
fileCT = joinpath(testdir, "CT_Explicit_Little")
fileMG = joinpath(testdir, "MG_Explicit_Little.zip")


# Don't download files if they already exist
if !isfile(fileMR) && !isfile(fileCT) && !isfile(fileMG)
download("http://www.barre.nom.fr/medical/samples/files/MR-MONO2-16-head.gz", fileMR*".gz")
download("http://www.barre.nom.fr/medical/samples/files/CT-MONO2-16-brain.gz", fileCT*".gz")
download("http://www.dclunie.com/images/pixelspacingtestimages.zip", fileMG)

run(`gunzip -f $(fileMR*".gz")`)
run(`gunzip -f $(fileCT*".gz")`)
run(`unzip -o $fileMG -d $testdir`)
const dicom_samples = Dict(
"CT_Explicit_Little.dcm" => "https://github.com/notZaki/DICOMSamples/raw/master/DICOMSamples/CT_Explicit_Little.dcm",
"CT_Implicit_Little_Headless_Retired.dcm" => "https://github.com/notZaki/DICOMSamples/raw/master/DICOMSamples/CT_Implicit_Little_Headless_Retired.dcm",
"MG_Explicit_Little.dcm" => "https://github.com/notZaki/DICOMSamples/raw/master/DICOMSamples/MG_Explicit_Little.dcm",
"MR_Explicit_Little_MultiFrame.dcm" => "https://github.com/notZaki/DICOMSamples/raw/master/DICOMSamples/MR_Explicit_Little_MultiFrame.dcm",
"MR_Implicit_Little.dcm" => "https://github.com/notZaki/DICOMSamples/raw/master/DICOMSamples/MR_Implicit_Little.dcm",
"MR_UnspecifiedLength.dcm" => "https://github.com/notZaki/DICOMSamples/raw/master/DICOMSamples/MR_UnspecifiedLength.dcm",
"OT_Implicit_Little_Headless.dcm" => "https://github.com/notZaki/DICOMSamples/raw/master/DICOMSamples/OT_Implicit_Little_Headless.dcm"
)

function download_dicom(filename; folder = data_folder)
@assert haskey(dicom_samples, filename)
url = dicom_samples[filename]
filepath = joinpath(folder, filename)
if !isfile(filepath)
download(url, filepath)
end
return filepath
end

# Load dicom data
dcmMR_partial = dcm_parse(fileMR, maxGrp=0x0008)
dcmMR = dcm_parse(fileMR)
dcmCT = dcm_parse(fileCT)
(dcmMG, vrMG) = dcm_parse(joinpath(testdir, "DISCIMG/IMAGES/MGIMAGEA"), true)
@testset "Reading DICOM" begin
fileMR = download_dicom("MR_Implicit_Little.dcm")
fileCT = download_dicom("CT_Explicit_Little.dcm")
fileMG = download_dicom("MG_Explicit_Little.dcm")

dcmMR_partial = dcm_parse(fileMR, maxGrp=0x0008)
dcmMR = dcm_parse(fileMR)
dcmCT = dcm_parse(fileCT)
(dcmMG, vrMG) = dcm_parse(fileMG, true)

@testset "Loading DICOM data" begin
@test dcmMR_partial[(0x0008,0x0060)] == "MR"
@test haskey(dcmMR_partial, (0x7FE0,0x0010)) == false

@test dcmMR[(0x0008,0x0060)] == "MR"
@test dcmCT[(0x0008,0x0060)] == "CT"
@test dcmMG[(0x0008,0x0060)] == "MG"
Expand All @@ -47,41 +52,44 @@ dcmCT = dcm_parse(fileCT)
@test dcmMR[(0x7FE0,0x0010)] == lookup(dcmMR, "Pixel Data")
end

# Define two output files for each dcm - data will be saved, reloaded, then saved again
outMR1 = joinpath(testdir,"outMR1.dcm")
outMR2 = joinpath(testdir,"outMR2.dcm")

outCT1 = joinpath(testdir,"outCT1.dcm")
outCT2 = joinpath(testdir,"outCT2.dcm")

outMG1 = joinpath(testdir,"outMG1.dcm")
outMG1b = joinpath(testdir,"outMG1b.dcm")
outMG2 = joinpath(testdir,"outMG2.dcm")

@testset "Writing DICOM data" begin
# No specific test, just test if file is saved without errors
@testset "Writing DICOM" begin
fileMR = download_dicom("MR_Implicit_Little.dcm")
fileCT = download_dicom("CT_Explicit_Little.dcm")
fileMG = download_dicom("MG_Explicit_Little.dcm")

dcmMR = dcm_parse(fileMR)
dcmCT = dcm_parse(fileCT)
(dcmMG, vrMG) = dcm_parse(fileMG, true)

# Define two output files for each dcm - data will be saved, reloaded, then saved again
outMR1 = joinpath(data_folder,"outMR1.dcm")
outMR2 = joinpath(data_folder,"outMR2.dcm")
outCT1 = joinpath(data_folder,"outCT1.dcm")
outCT2 = joinpath(data_folder,"outCT2.dcm")
outMG1 = joinpath(data_folder,"outMG1.dcm")
outMG1b = joinpath(data_folder,"outMG1b.dcm")
outMG2 = joinpath(data_folder,"outMG2.dcm")

# Write DICOM files
outIO = open(outMR1, "w+"); dcm_write(outIO,dcmMR); close(outIO)
outIO = open(outCT1, "w+"); dcm_write(outIO,dcmCT); close(outIO)
outIO = open(outMG1, "w+"); dcm_write(outIO,dcmMG,vrMG); close(outIO)
dcm_write(outMG1b,dcmMG,vrMG)
end

# Load saved DICOM data
dcmMR1 = dcm_parse(outMR1)
dcmCT1 = dcm_parse(outCT1)
(dcmMG1, vrMG1) = dcm_parse(outMG1, true)

@testset "Consistence of Reading/Writing data" begin
# Confirm that re-loading/saving leads to same file
# Reading DICOM files which were written from previous step
dcmMR1 = dcm_parse(outMR1)
dcmCT1 = dcm_parse(outCT1)
(dcmMG1, vrMG1) = dcm_parse(outMG1, true)
# Write DICOM files which were re-read from previous step
outIO = open(outMR2, "w+"); dcm_write(outIO,dcmMR1); close(outIO)
outIO = open(outCT2, "w+"); dcm_write(outIO,dcmCT1); close(outIO)
outIO = open(outMG2, "w+"); dcm_write(outIO,dcmMG1, vrMG1); close(outIO)

# Test consistency of written files after the write-read-write cycle
@test read(outMR1)==read(outMR2)
@test read(outCT1)==read(outCT2)
@test read(outMG1)==read(outMG2)

# Repeat first tests on reloaded data
# Repeat first testset on written data
@test dcmMR1[(0x0008,0x0060)] == "MR"
@test dcmCT1[(0x0008,0x0060)] == "CT"
@test dcmMG1[(0x0008,0x0060)] == "MG"
Expand All @@ -95,74 +103,50 @@ dcmCT1 = dcm_parse(outCT1)
@test dcmMR1[(0x7FE0,0x0010)] == lookup(dcmMR, "Pixel Data")
end

# TEST SET 2: Reading uncommon datasets

# 1. Loading DICOM file with missing header
fileOT = joinpath(testdir, "OT_Implicit_Little_Headless")
if !isfile(fileOT)
download("http://www.barre.nom.fr/medical/samples/files/OT-MONO2-8-a7.gz", fileOT*".gz")
run(`gunzip -f $(fileOT*".gz")`)
end

dcmOT = dcm_parse(fileOT, header=false)

# 2. Loading DICOM file with missing header and retired DICOM elements
fileCT = joinpath(testdir, "CT-Implicit_Little_Headless_Retired")
if !isfile(fileCT)
download("http://www.barre.nom.fr/medical/samples/files/CT-MONO2-12-lomb-an2.gz", fileCT*".gz")
run(`gunzip -f $(fileCT*".gz")`)
end

# 2a. With user-supplied VRs
dVR_CTa = Dict(
(0x0008,0x0010) => "SH",
(0x0008,0x0040) => "US",
(0x0008,0x0041) => "LO",
(0x0018,0x1170) => "DS",
(0x0020,0x0030) => "DS",
(0x0020,0x0035) => "DS",
(0x0020,0x0050) => "DS",
(0x0020,0x0070) => "LO",
(0x0028,0x0005) => "US",
(0x0028,0x0040) => "CS",
(0x0028,0x0200) => "US")
dcmCTa = dcm_parse(fileCT, header=false, dVR=dVR_CTa);

# 2b. With a master VR which skips elements
# Here we skip any element where lookup_vr() fails
# And we also force (0x0018,0x1170) to be read as float instead of integer
dVR_CTb = Dict( (0x0000,0x0000) => "", (0x0018,0x1170) => "DS")
dcmCTb = dcm_parse(fileCT, header=false, dVR=dVR_CTb);

# 3. Loading DICOM file containing multiple frames
fileMR_multiframe = joinpath(testdir, "MR-Explicit_Little_MultiFrame")
if !isfile(fileMR_multiframe)
download("http://www.barre.nom.fr/medical/samples/files/MR-MONO2-8-16x-heart.gz", fileMR_multiframe*".gz")
run(`gunzip -f $(fileMR_multiframe*".gz")`)
end
dcmMR_multiframe = dcm_parse(fileMR_multiframe)

# 4. Load DICOM with unspecified_length()
fileMR_UnspecifiedLength = joinpath(testdir, "MR-UnspecifiedLength")
if !isfile(fileMR_UnspecifiedLength)
download("https://drive.google.com/uc?export=download&id=1lm0750H-1O22O7Bqy0yfq0FK_vDrqC7-", fileMR_UnspecifiedLength)
end
dcmMR_UnspecifiedLength = dcm_parse(fileMR_UnspecifiedLength)

@testset "Loading uncommon DICOM data" begin
@testset "Uncommon DICOM" begin
# 1. DICOM file with missing header
fileOT = download_dicom("OT_Implicit_Little_Headless.dcm")
dcmOT = dcm_parse(fileOT, header=false)
@test dcmOT[(0x0008,0x0060)] == "OT"


# 2. DICOM file with missing header and retired DICOM elements
fileCT = download_dicom("CT_Implicit_Little_Headless_Retired.dcm")
# 2a. Read with user-supplied VRs
dVR_CTa = Dict(
(0x0008,0x0010) => "SH",
(0x0008,0x0040) => "US",
(0x0008,0x0041) => "LO",
(0x0018,0x1170) => "DS",
(0x0020,0x0030) => "DS",
(0x0020,0x0035) => "DS",
(0x0020,0x0050) => "DS",
(0x0020,0x0070) => "LO",
(0x0028,0x0005) => "US",
(0x0028,0x0040) => "CS",
(0x0028,0x0200) => "US")
dcmCTa = dcm_parse(fileCT, header=false, dVR=dVR_CTa);
# 2b. Read with a master VR which skips elements
# Here we skip any element where lookup_vr() fails
# And we also force (0x0018,0x1170) to be read as float instead of integer
dVR_CTb = Dict( (0x0000,0x0000) => "", (0x0018,0x1170) => "DS")
dcmCTb = dcm_parse(fileCT, header=false, dVR=dVR_CTb);
@test dcmCTa[(0x0008,0x0060)] == "CT"
@test dcmCTb[(0x0008,0x0060)] == "CT"
@test haskey(dcmCTa, (0x0028,0x0040)) # dcmCTa should contain retired element
@test !haskey(dcmCTb, (0x0028,0x0040)) # dcmCTb skips retired elements

# 3. DICOM file containing multiple frames
fileMR_multiframe = download_dicom("MR_Explicit_Little_MultiFrame.dcm")
dcmMR_multiframe = dcm_parse(fileMR_multiframe)
@test dcmMR_multiframe[(0x0008,0x0060)] == "MR"

# 4. DICOM with unspecified_length()
fileMR_UnspecifiedLength = download_dicom("MR_UnspecifiedLength.dcm")
dcmMR_UnspecifiedLength = dcm_parse(fileMR_UnspecifiedLength)
@test size(dcmMR_UnspecifiedLength[tag"Pixel Data"]) === (256, 256, 27)
end

@testset "tag" begin
@testset "Test tag macro" begin
@test tag"Modality" === (0x0008, 0x0060) ===
DICOM.fieldname_dict["Modality"]
@test tag"Shutter Overlay Group" === (0x0018, 0x1623) ===
Expand Down