Merge pull request #88 from AaronGhost/PassSQAuxVR

Pass aux_vr to SQ elements in dcm_write

.github/workflows/ci.yml

@@ -10,9 +10,8 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.0'
-          - '1'
-          - 'nightly'
+          - "1"
+          - "nightly"
         os:
           - ubuntu-latest
           - macOS-latest

Project.toml

@@ -1,12 +1,13 @@
 name = "DICOM"
 uuid = "a26e6606-dd52-5f6a-a97f-4f611373d757"
-version = "0.10.1"
+version = "0.11.0"
 
 [compat]
-julia = "0.7, 1"
+julia = "1.6"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 
 [targets]
-test = ["Test"]
+test = ["Test", "Downloads"]

src/DICOM.jl

@@ -592,7 +592,7 @@ function write_element(st::IO, gelt::Tuple{UInt16,UInt16}, data, is_explicit, au
 
     if vr == "SQ"
         vr = is_explicit ? vr : empty_vr
-        return dcm_store(st, gelt, s -> sequence_write(s, map(d -> d.meta, data), is_explicit), vr)
+        return dcm_store(st, gelt, s -> sequence_write(s, map(d -> d.meta, data), is_explicit, aux_vr), vr)
     end
 
     # Pack data into array container. This is to undo "data = data[1]" from read_element().
@@ -658,27 +658,27 @@ function dcm_store(st::IO, gelt::Tuple{UInt16,UInt16}, writef::Function, vr::Str
         sz += 1
     end
     seek(st, p)
-    write(st, convert(lentype, max(0, sz)))
+    vr == "SQ" || gelt == (0xFFFE, 0xE000) ? write(st, convert(lentype, 0xffffffff)) : write(st, convert(lentype, max(0, sz)))
     seek(st, endp)
     if szWasOdd
-        write(st, UInt8(0))
+        vr in ("AE", "CS", "SH", "LO", "PN", "DA", "DT", "TM") ? write(st, UInt8(0x20)) : write(st, UInt8(0))
     end
 end
 
-sequence_write(st::IO, items::Array{Any,1}, evr::Bool) =
-    sequence_write(st, convert(Array{Dict{Tuple{UInt16,UInt16},Any},1}, items), evr)
-function sequence_write(st::IO, items::Array{Dict{Tuple{UInt16,UInt16},Any},1}, evr)
+sequence_write(st::IO, items::Array{Any,1}, evr::Bool, aux_vr::Dict{Tuple{UInt16, UInt16}}) =
+    sequence_write(st, convert(Array{Dict{Tuple{UInt16,UInt16},Any},1}, items), evr, aux_vr)
+function sequence_write(st::IO, items::Array{Dict{Tuple{UInt16,UInt16},Any},1}, evr, aux_vr::Dict{Tuple{UInt16, UInt16}})
     for subitem in items
         if length(subitem) > 0
-            dcm_store(st, (0xFFFE, 0xE000), s -> sequence_item_write(s, subitem, evr))
+            dcm_store(st, (0xFFFE, 0xE000), s -> sequence_item_write(s, subitem, evr, aux_vr))
         end
     end
     write(st, UInt16[0xFFFE, 0xE0DD, 0x0000, 0x0000])
 end
 
-function sequence_item_write(st::IO, items::Dict{Tuple{UInt16,UInt16},Any}, evr)
+function sequence_item_write(st::IO, items::Dict{Tuple{UInt16,UInt16},Any}, evr, aux_vr::Dict{Tuple{UInt16, UInt16}})
     for gelt in sort(collect(keys(items)))
-        write_element(st, gelt, items[gelt], evr, empty_dcm_dict)
+        write_element(st, gelt, items[gelt], evr, aux_vr)
     end
     write(st, UInt16[0xFFFE, 0xE00D, 0x0000, 0x0000])
 end

test/runtests.jl

@@ -1,5 +1,6 @@
 using Test
 using DICOM
+using Downloads
 
 const data_folder = joinpath(@__DIR__, "testdata")
 if !isdir(data_folder)
@@ -26,15 +27,15 @@ const dicom_samples = Dict(
     "US_Explicit_Big_RGB.dcm" =>
         "https://github.com/notZaki/DICOMSamples/raw/master/DICOMSamples/US_Explicit_Big_RGB.dcm",
     "DX_Implicit_Little_Interleaved.dcm" =>
-        "https://github.com/OHIF/viewer-testdata/raw/master/dcm/zoo-exotic/5.dcm",
+        "https://github.com/notZaki/DICOMSamples/raw/master/DICOMSamples/DX_Implicit_Little_Interleaved.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)
+        Downloads.download(url, filepath)
     end
     return filepath
 end
@@ -233,8 +234,8 @@ end
     end
 
     # First, test the isdicom() function
-    fileDX = download_dicom("DX_Implicit_Little_Interleaved.dcm")
-    @test DICOM.isdicom(fileDX) == true
+    fileCT = download_dicom("CT_JPEG70.dcm")
+    @test DICOM.isdicom(fileCT) == true
     @test DICOM.isdicom(notdicomfile) == false
 
     # Second, test if all valid dicom file can be parsed
@@ -255,3 +256,53 @@ end
     @test macroexpand(Main, :(tag"Modality")) === (0x0008, 0x0060)
     @test_throws LoadError macroexpand(Main, :(tag"nonsense"))
 end
+
+@testset "Test VR in Sequence" begin
+    # Test auxillary VR passed to nested tags
+    fileMG = download_dicom("MG_Explicit_Little.dcm")
+    dcmMG = dcm_parse(fileMG)
+    # Set value of CodeMeaning for both tags to something arbitrary
+    codemeaning_vr = Dict{Tuple{UInt16, UInt16}, String}((0x008, 0x104) => "US")
+    dcmMG[(0x0008, 0x2218)][1][(0x0008, 0x0104)] = 0x0001
+    dcmMG[(0x0054, 0x0220)][1][(0x0008, 0x0104)] = 0x0002
+
+    outMG3 = joinpath(data_folder, "outMG3.dcm")
+    dcm_write(outMG3, dcmMG; aux_vr = codemeaning_vr)
+    dcmMG3 = dcm_parse(outMG3)
+    @test dcmMG3[(0x0008, 0x2218)][1][(0x0008, 0x0104)] == 0x0001
+    @test dcmMG3[(0x0054, 0x0220)][1][(0x0008, 0x0104)] == 0x0002
+end
+
+function write_to_string(writef)
+    io = IOBuffer()
+    writef(io)
+    return String(take!(io))
+end
+
+@testset "Padding string values" begin
+    empty_vr_dict = Dict{Tuple{UInt16, UInt16}, String}()
+    # Test that UI strings are padded with '\0' to even length
+    SOPClassUID = write_to_string(io -> DICOM.write_element(io, (0x0008, 0x0016), "1.2.840.10008.5.1.4.1.1.4", true, empty_vr_dict))
+    @test length(SOPClassUID) % 2 == 0
+    @test SOPClassUID[end] == '\0'
+    # Test that SH strings are padded with ' ' to even length
+    StudyDescription = write_to_string(io -> DICOM.write_element(io, (0x0008, 0x1030), "BestImageEver", true, empty_vr_dict))
+    @test length(StudyDescription) % 2 == 0
+    @test StudyDescription[end] == ' '
+end
+
+@testset "Writing Sequence" begin
+    empty_vr_dict = Dict{Tuple{UInt16, UInt16}, String}()
+    # Setup internal SQ DICOMData
+    sq_meta = Dict{Tuple{UInt16, UInt16}, Any}([(0x0008, 0x0100) => "UNDEFINED", (0x0008, 0x010b) => 'N', (0x0008, 0x0104) => "UNDEFINED"])
+    sq_el = DICOM.DICOMData(sq_meta, :little, true, empty_vr_dict)
+
+    # Setup external SQ DICOMData
+    meta = Dict{Tuple{UInt16, UInt16}, Any}((0x0040, 0x0260) => [sq_el])
+    el = DICOM.DICOMData(meta, :little, true, empty_vr_dict)
+
+    PerformedProtocolSequence = write_to_string(io -> DICOM.write_element(io, (0x0040, 0x0260), el[(0x0040, 0x0260)], true, empty_vr_dict))
+    # Check that the length is (0xffffffff) for undefined length SQ
+    @test PerformedProtocolSequence[9:12] == "\xff\xff\xff\xff"
+    @test PerformedProtocolSequence[end-7:end] == "\xfe\xff\xdd\xe0\x00\x00\x00\x00"
+end