Merge pull request #635 from JuliaHealth/pulseq-150-warn

Warn about Pulseq 1.5.0 support gap

Author: cncastillo

KomaMRIFiles/Project.toml

@@ -1,7 +1,7 @@
 name = "KomaMRIFiles"
 uuid = "fcf631a6-1c7e-4e88-9e64-b8888386d9dc"
 authors = ["Carlos Castillo Passi <cncastillo@uc.cl>"]
-version = "0.9.4"
+version = "0.9.5"
 
 [deps]
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"

KomaMRIFiles/src/Sequence/Pulseq.jl

@@ -8,20 +8,22 @@ read_version Read the [VERSION] section of a sequence file.
    identifier of an open MR sequence file and return it
 """
 function read_version(io)
-    major =    @scanf(readline(io), "major %i", Int)[end]
-    minor =    @scanf(readline(io), "minor %i", Int)[end]
-    revision = @scanf(readline(io), "revision %i", Int)[end]
-
-    version_combined = 1_000_000*major+1_000*minor+revision
-
-    @assert major == 1 "Unsupported version_major $major"
-    if     version_combined < 1002000
-        @error "Unsupported version $major.$minor.$revision, only file format revision 1.2.0 and above are supported"
-    elseif version_combined < 1003001
-        @warn "Loading older Pulseq format file (version $major.$minor.$revision) some code may not function as expected"
+    pulseq_version = VersionNumber(
+        @scanf(readline(io), "major %i", Int)[end],
+        @scanf(readline(io), "minor %i", Int)[end],
+        @scanf(readline(io), "revision %i", Int)[end],
+    )
+
+    @assert pulseq_version.major == 1 "Unsupported version_major $(pulseq_version.major)"
+    if     pulseq_version < v"1.2.0"
+        @error "Unsupported Pulseq $(pulseq_version), only file format revision 1.2.0 and above are supported"
+    elseif pulseq_version < v"1.3.1"
+        @warn "Loading older Pulseq $(pulseq_version); some code may not function as expected"
+    elseif pulseq_version >= v"1.5.0"
+        @warn "Pulseq $(pulseq_version) not yet supported by this KomaMRIFiles release. Track progress at https://github.com/JuliaHealth/KomaMRI.jl/pull/614"
     end
 
-    major, minor, revision, version_combined
+    pulseq_version
 end
 
 """
@@ -76,12 +78,12 @@ read_blocks Read the [BLOCKS] section of a sequence file.
    library=read_blocks(fid) Read blocks from file identifier of an
    open MR sequence file and return the event table.
 """
-function read_blocks(io, blockDurationRaster, version_combined)
+function read_blocks(io, blockDurationRaster, pulseq_version)
     eventTable = Dict{Int64, Vector{Int64}}()
     blockDurations = Dict{Int64, Float64}()
     delayIDs_tmp = Dict{Int64, Float64}()
     while true
-        if version_combined <= 1002001
+        if pulseq_version <= v"1.2.1"
             NumberBlockEvents = 7
         else
             NumberBlockEvents = 8
@@ -92,13 +94,13 @@ function read_blocks(io, blockDurationRaster, version_combined)
         blockEvents = parse.(Int64, split(read_event))
 
         if blockEvents[1] != 0
-            if version_combined <= 1002001
+            if pulseq_version <= v"1.2.1"
                 eventTable[blockEvents[1]] = Int64[0; blockEvents[3:end]...; 0]
             else
                 eventTable[blockEvents[1]] = Int64[0; blockEvents[3:end]...]
             end
 
-            if version_combined >= 1004000
+            if pulseq_version >= v"1.4.0"
                 blockDurations[blockEvents[1]] = blockEvents[2]*blockDurationRaster
             else
                 delayIDs_tmp[blockEvents[1]] = blockEvents[2]
@@ -375,9 +377,7 @@ julia> plot_seq(seq)
 """
 function read_seq(filename)
     @info "Loading sequence $(basename(filename)) ..."
-    version_combined = 0
-    version_major = 0
-    version_minor = 0
+    pulseq_version = v"0.0.0"
     gradLibrary = Dict()
     def = Dict()
     signature = ""
@@ -403,21 +403,21 @@ function read_seq(filename)
             elseif     section == "[DEFINITIONS]"
                 def = read_definitions(io)
             elseif  section == "[VERSION]"
-                version_major, version_minor, _, version_combined = read_version(io)
+                pulseq_version = read_version(io)
             elseif  section == "[BLOCKS]"
-                if version_combined == 0
+                if pulseq_version == v"0.0.0"
                     @error "Pulseq file MUST include [VERSION] section prior to [BLOCKS] section"
                 end
-                blockEvents, blockDurations, delayInd_tmp = read_blocks(io, def["BlockDurationRaster"], version_combined)
+                blockEvents, blockDurations, delayInd_tmp = read_blocks(io, def["BlockDurationRaster"], pulseq_version)
             elseif  section == "[RF]"
-                if version_combined >= 1004000
+                if pulseq_version >= v"1.4.0"
                     rfLibrary = read_events(io, [1/γ 1 1 1 1e-6 1 1]) # this is 1.4.x format
                 else
                     rfLibrary = read_events(io, [1/γ 1 1 1e-6 1 1]) # this is 1.3.x and below
                     # we will have to scan through the library later after all the shapes have been loaded
                 end
             elseif  section == "[GRADIENTS]"
-                if version_combined >= 1004000
+                if pulseq_version >= v"1.4.0"
                     gradLibrary = read_events(io, [1/γ 1 1 1e-6]; type='g', eventLibrary=gradLibrary) # this is 1.4.x format
                 else
                     gradLibrary = read_events(io, [1/γ 1 1e-6];   type='g', eventLibrary=gradLibrary) # this is 1.3.x and below
@@ -427,12 +427,12 @@ function read_seq(filename)
             elseif  section == "[ADC]"
                 adcLibrary = read_events(io, [1 1e-9 1e-6 1 1])
             elseif  section == "[DELAYS]"
-                if version_combined >= 1004000
+                if pulseq_version >= v"1.4.0"
                     @error "Pulseq file revision 1.4.0 and above MUST NOT contain [DELAYS] section"
                 end
                 tmp_delayLibrary = read_events(io, 1e-6);
             elseif  section == "[SHAPES]"
-                shapeLibrary = read_shapes(io, (version_major==1 && version_minor<4))
+                shapeLibrary = read_shapes(io, (pulseq_version.major == 1 && pulseq_version.minor < 4))
             elseif  section == "[EXTENSIONS]"
                 extensionLibrary = read_extension_blocks(io)
             elseif  section == "[SIGNATURE]"
@@ -465,7 +465,7 @@ function read_seq(filename)
         end
     end
     # fix blocks, gradients and RF objects imported from older versions
-    if version_combined < 1004000
+    if pulseq_version < v"1.4.0"
         # scan through the RF objects
         for i = 0:length(rfLibrary)-1
             rfLibrary[i]["data"] = [rfLibrary[i]["data"][1:3]' 0.0 rfLibrary[i]["data"][4:end]']
@@ -531,7 +531,7 @@ function read_seq(filename)
     seq.DEF = merge(obj["definitions"], seq.DEF)
     # Koma specific details for reconstrucion
     seq.DEF["FileName"] = basename(filename)
-    seq.DEF["PulseqVersion"] = version_combined
+    seq.DEF["PulseqVersion"] = pulseq_version
     seq.DEF["signature"] = signature
     # Guessing recon dimensions
     seq.DEF["Nx"] = get(seq.DEF, "Nx", maximum(adc.N for adc = seq.ADC))

KomaMRIFiles/test/runtests.jl

@@ -10,22 +10,22 @@ using TestItems, TestItemRunner, KomaMRIBase
         pth = @__DIR__
         seq = @suppress read_seq(pth*"/test_files/epi.seq") #Pulseq v1.4.0, RF arbitrary
         @test seq.DEF["FileName"] == "epi.seq"
-        @test seq.DEF["PulseqVersion"] ≈ 1004000
+        @test seq.DEF["PulseqVersion"] == v"1.4.0"
         @test seq.DEF["signature"] == "67ebeffe6afdf0c393834101c14f3990"
 
         seq = @suppress read_seq(pth*"/test_files/spiral.seq") #Pulseq v1.4.0, RF arbitrary
         @test seq.DEF["FileName"] == "spiral.seq"
-        @test seq.DEF["PulseqVersion"] ≈ 1004000
+        @test seq.DEF["PulseqVersion"] == v"1.4.0"
         @test seq.DEF["signature"] == "efc5eb7dbaa82aba627a31ff689c8649"
 
         seq = @suppress read_seq(pth*"/test_files/epi_JEMRIS.seq") #Pulseq v1.2.1
         @test seq.DEF["FileName"] == "epi_JEMRIS.seq"
-        @test seq.DEF["PulseqVersion"] ≈ 1002001
+        @test seq.DEF["PulseqVersion"] == v"1.2.1"
         @test seq.DEF["signature"] == "f291a24409c3e8de01ddb93e124d9ff2"
 
         seq = @suppress read_seq(pth*"/test_files/radial_JEMRIS.seq") #Pulseq v1.2.1
         @test seq.DEF["FileName"] == "radial_JEMRIS.seq"
-        @test seq.DEF["PulseqVersion"] ≈ 1002001
+        @test seq.DEF["PulseqVersion"] == v"1.2.1"
         @test seq.DEF["signature"] == "e827cfff4436b65a6341a4fa0f6deb07"
 
         # Test Pulseq compression-decompression