merge

Project.toml

@@ -1,7 +1,7 @@
 name = "MPIFiles"
 uuid = "371237a9-e6c1-5201-9adb-3d8cfa78fa9f"
 authors = ["Tobias Knopp <tobias@knoppweb.de>"]
-version = "0.11.8"
+version = "0.11.10"
 
 [deps]
 AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"

README.md

@@ -9,5 +9,3 @@ MPIFiles.jl is a Julia package for loading and storing magnetic particle imaging
 [![Build status](https://github.com/MagneticParticleImaging/MPIFiles.jl/workflows/CI/badge.svg)](https://github.com/MagneticParticleImaging/MPIFiles.jl/actions)
 
 [![codecov.io](http://codecov.io/github/MagneticParticleImaging/MPIFiles.jl/coverage.svg?branch=master)](http://codecov.io/github/MagneticParticleImaging/MPIFiles.jl?branch=master)
-
-[![Build status](https://ci.appveyor.com/api/projects/status/mvkx2xoi21jssbin/branch/master?svg=true)](https://ci.appveyor.com/project/tknopp/mpifiles-jl/branch/master)

src/DatasetStore/MDFDatasetStore.jl

@@ -1,4 +1,4 @@
-export MDFDatasetStore, MDFStore, addStudy, getMDFStudyFolderName, calibdir, getMDFStore
+export MDFDatasetStore, MDFStore, addStudy, getMDFStudyFolderName, calibdir, getMDFStore, getCalibStudy
 
 struct MDFDatasetStore <: DatasetStore
   path::String
@@ -9,6 +9,7 @@ struct MDFDatasetStore <: DatasetStore
     mkpath(joinpath(path,"measurements"))
     mkpath(joinpath(path,"reconstructions"))
     mkpath(joinpath(path,"calibrations"))
+    #try_chmod(joinpath(path,"path"), 0o777, recursive=true) # we should get rid of this
     return new(path)
   end
 end

src/MDFInMemory.jl

@@ -892,13 +892,16 @@ function checkConsistency(mdf::MDFv2InMemory)
     if !(fieldtype == MDFv2Variables || fieldname == :custom)
       # At the moment, this should be a Union
       fieldtype = (fieldtype.b <: MDFv2InMemoryPart) ? fieldtype.b : fieldtype.a
+
       @debug "Checking consistency of `$fieldname`."
 
       field = getproperty(mdf, fieldname)
       @assert !ismissing(field) "The field `$fieldname` is missing in the given in-memory MDF."
-
-      checkMissing(field)
-      check(field, mdf.variables)
+
+      if !isnothing(field) # Only optional fields can be `nothing`
+        checkMissing(field)
+        check(field, mdf.variables)
+      end
 
       # Check subgroups of acquisition
       if fieldtype == MDFv2Acquisition
@@ -1224,7 +1227,11 @@ function saveasMDF(file::HDF5.File, mdf::MDFv2InMemory; failOnInconsistent::Bool
     try
       checkConsistency(mdf)
     catch e
-      @warn "There is an inconsistency in the given in-memory MDF. The message is: `$(e.msg)`."
+      if e isa AssertionError
+        @warn "There is an inconsistency in the given in-memory MDF. The message is: `$(e.msg)`."
+      else
+        rethrow()
+      end
     end
   end
 

src/Measurements.jl

@@ -267,7 +267,7 @@ function getMeasurements(f::MPIFile, neglectBGFrames=true;
 
     J = size(data,1)
     dataF = rfft(data, 1)
-    dataF ./= tf
+    dataF[2:end,:,:,:] ./= tf[2:end,:,:,:]
     @warn "This measurement has been corrected with a Transfer Function. Name of TF: $(rxTransferFunctionFileName(f))"
     if inductionFactor != nothing
        	for k=1:length(inductionFactor)
@@ -309,7 +309,7 @@ function getMeasurementsFD(f::MPIFile, args...;
   if tfCorrection && !measIsTFCorrected(f)
     tf = rxTransferFunction(f)
     inductionFactor = rxInductionFactor(f)
-    data ./= tf
+    data[2:end,:,:,:] ./= tf[2:end,:,:,:]
     @warn "This measurement has been corrected with a Transfer Function. Name of TF: $(rxTransferFunctionFileName(f))"
     if inductionFactor != nothing
        	for k=1:length(inductionFactor)

src/Positions/Positions.jl

@@ -176,8 +176,10 @@ function getindex(grid::RegularGridPositions, i::Integer)
     idx = [i]
   elseif length(grid.shape) == 2
     idx = collect(Tuple((CartesianIndices(tuple(grid.shape[1],grid.shape[2])))[i]))
-  else
+  elseif length(grid.shape) == 3
     idx = collect(Tuple((CartesianIndices(tuple(grid.shape[1],grid.shape[2],grid.shape[3])))[i]))
+  else
+    idx = collect(Tuple((CartesianIndices(tuple(grid.shape...)))[i]))
   end
 
   for d=1:length(idx)
@@ -303,10 +305,11 @@ end
 
 function indexPermutation(grid::MeanderingGridPositions, i::Integer)
   dims = tuple(shape(grid)...)
+  ndims = length(dims)
   idx = collect(Tuple(CartesianIndices(dims)[i]))
-    for d=2:3
-      if isodd(sum(idx[d:3])-length(idx[d:3]))
-      idx[d-1] = shape(grid)[d-1] + 1 - idx[d-1]
+    for d=1:ndims-1
+      if isodd(sum(idx[d+1:end])-(ndims-d))
+      idx[d] = -idx[d] + shape(grid)[d] + 1
     end
   end
   linidx = (LinearIndices(dims))[idx...]

test/General.jl

@@ -165,7 +165,7 @@
       @test size(getSystemMatrix(sm,1:10)) == (1936,10)
       @test size(getSystemMatrix(sm,1:10,loadasreal=true)) == (1936,20)
       @test size(getSystemMatrix(sm,1:10,bgCorrection=true)) == (1936,10)
-      # test on the data level if the conversion was successfull
+      # test on the data level if the conversion was successful
       SNRThresh = 2
       freq = filterFrequencies(smBruker,SNRThresh=SNRThresh)
       SBruker = getSystemMatrix(smBruker,frequencies=freq)

test/MDFInMemory.jl

@@ -412,6 +412,12 @@ end
     # See also: https://github.com/JuliaLang/julia/issues/18780
     @test checkConsistency(mdf) # This call has a side-effect on the variables!
 
+    # Check if non-required fields make consistency checking fail
+    tracer = mdf.tracer
+    mdf.tracer = nothing
+    @test checkConsistency(mdf)
+    mdf.tracer = tracer
+
     @testset "Derived variables" begin
       @test mdf.variables.A == A
       @test mdf.variables.N == N