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Merge pull request #36 from notZaki/updateTestURL
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Update URLs in tests
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@notZaki
notZaki authored Oct 14, 2019
2 parents ba85142 + 766c594 commit 39045c5
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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) ===
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