Use ASCCONV from Phoenix header (#5)

* Overwrite metadata from Phoenix' ASCCONV (previously only extract MeasYaps) if same key found since MeasYaps is sometimes inconsistent with others section, especially in frequency.

* Log the difference in warning.

src/io_twix.jl

@@ -333,13 +333,32 @@ function load_twix(io::IO; header_only=false, acquisition_filter=(acq)->true,
     @debug "Header section names" keys(header_sections)
     metadata = Dict{String,Any}()
     try
+        phoenix_ascconv = match(r"(### ASCCONV BEGIN.*### ASCCONV END ###)"s,
+                                header_sections["Phoenix"]).captures[1]
         yaps_meta = parse_header_yaps(header_sections["MeasYaps"])
+        phoenix_ascconv_meta = parse_header_yaps(phoenix_ascconv)
+
+        # Check if the same key has different value in yaps and phoenix to warn user
+        differences = Dict()
+        for k in intersect(Set(keys(yaps_meta)), Set(keys(phoenix_ascconv_meta)))
+            if yaps_meta[k] != phoenix_ascconv_meta[k]
+                differences[k] = (MeasYapsASCCONV=yaps_meta[k],
+                                  PhoenixASCCONV=phoenix_ascconv_meta[k])
+            end
+        end
+        if length(differences) > 0
+            @warn """
+                  Different values found in MeasYaps and Phoenix ASCCONV section. As per
+                  our testing in getting the correct frequency, MeasYaps sometimes is not
+                  consistent with other sections, so this metadata is extracted from Phoenix.
+                  """ differences
+        end
         dicom_meta = match_xprot_header(header_sections["Dicom"], "Dicom.",
                                         ["SoftwareVersions", "DeviceSerialNumber", "InstitutionName", "Manufacturer", "ManufacturersModelName"])
         meas_meta  = match_xprot_header(header_sections["Meas"], "Meas.",
                                         ["tReferenceImage0", "tReferenceImage1", "tReferenceImage2",
                                          "tFrameOfReference"])
-        metadata = merge(metadata, yaps_meta, dicom_meta, meas_meta)
+        metadata = merge(metadata, yaps_meta, phoenix_ascconv_meta, dicom_meta, meas_meta)
     catch exc
         @error "Could not parse header metadata" exception=(exc,catch_backtrace())
     end

test/io_twix.jl

@@ -85,6 +85,7 @@ end
 
 @testset "twix quality control" begin
     twix = @test_logs (Logging.Warn,r"Unexpected empty meas packet") #=
+               =# (Logging.Warn,r"Different values found in MeasYaps") #=
                =# load_twix("twix/sub-SiemensBrainPhantom_seq-svslcosy_incomplete.twix")
     @test MagneticResonanceSignals.AcquisitionsIncomplete in twix.quality_control
 
@@ -99,6 +100,7 @@ end
     truncated_twix = copy(valid_twix_bytes)
     truncated_twix = truncated_twix[1:900_000]
     twix = @test_logs (Logging.Warn,r"Twix acquisition truncated at position 900000") #=
+        =# (Logging.Warn,r"Different values found in MeasYaps") #=
         =# load_twix(IOBuffer(truncated_twix))
     @test MagneticResonanceSignals.AcquisitionsIncomplete in twix.quality_control
 end

test/mr_load.jl

@@ -2,7 +2,8 @@ using Logging
 
 @testset "mr_load integration test" begin
     # TODO: This is far too trivial! should get / generate some better test data.
-    cosy = @test_logs (:warn,r"Sequence.*is not one of the versions I recognize"s) #=
+    cosy = @test_logs (:warn,r"Different values found in MeasYaps") #=
+        =# (:warn,r"Sequence.*is not one of the versions I recognize"s) #=
         =# mr_load("twix/sub-SiemensBrainPhantom_seq-svslcosy_inc-1.twix")
 
     @test size(cosy.lcosy_scans) == (1,1)

test/processing.jl

@@ -24,7 +24,7 @@ end
 end
 
 @testset "lcosy" begin
-    lcosy = @test_logs (:warn,) mr_load("twix/sub-SiemensBrainPhantom_seq-svslcosy_inc-1.twix")
+    lcosy = @test_logs (:warn,) (:warn,) mr_load("twix/sub-SiemensBrainPhantom_seq-svslcosy_inc-1.twix")
 
     signal = simple_averaging(lcosy)
     @test size(signal) == (2048,1)