Merge remote-tracking branch 'origin/master' into JA/patchBrukerIMT

.github/dependabot.yml

@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/ci.yml

@@ -26,11 +26,11 @@ jobs:
           - x64
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
         with:
@@ -43,15 +43,15 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           file: lcov.info
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
           version: '1'
       - run: |

Project.toml

@@ -1,7 +1,7 @@
 name = "MPIFiles"
 uuid = "371237a9-e6c1-5201-9adb-3d8cfa78fa9f"
 authors = ["Tobias Knopp <[email protected]>"]
-version = "0.15.0"
+version = "0.15.3"
 
 [deps]
 AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"

src/DatasetStore/SFDatabase.jl

@@ -111,8 +111,8 @@ function _innerGenerateSFDatabase(A,i,sf,b)
   end
   N = calibSize(b)
   A[i,6] = N[1]
-  A[i,7] = N[2]
-  A[i,8] = N[3]
+  A[i,7] = try N[2]; catch; 0 end 
+  A[i,8] = try N[3]; catch; 0 end
   A[i,9] = rxBandwidth(b) / 1e6
   A[i,10] = tracerName(b)[1]
   A[i,11] = tracerBatch(b)[1]

src/Derived.jl

@@ -138,7 +138,13 @@ function measDataTD(f, frames=1:acqNumFrames(f), periods=1:acqNumPeriodsPerFrame
   end
 
   if measIsFourierTransformed(f)
-    dataTD = irfft(data2, rxNumSamplingPoints(f), 1)
+    if measIsFrequencySelection(f)
+      dataPadded = zeros(eltype(data2), (rxNumFrequencies(f), size(data2, 2), size(data2, 3), size(data2, 4)))
+      dataPadded[measFrequencySelection(f), :, :, :] .= data2
+      dataTD = irfft(dataPadded, rxNumSamplingPoints(f), 1)
+    else
+      dataTD = irfft(data2, rxNumSamplingPoints(f), 1)
+    end
   else
     dataTD = data2
   end

src/FrequencyFilter.jl

@@ -68,7 +68,7 @@ function filterFrequencies(f::MPIFile; SNRThresh=-1, minFreq=0,
     idx = measIsFrequencySelection(f) ? measFrequencySelection(f) : idx = 1:nFreq
 
     SNRAll = calibSNR(f)
-    if SNRAll != nothing
+    if !isnothing(SNRAll)
       SNR[idx,:] = SNRAll[:,:,1]
     end
   end

src/MDF.jl

@@ -159,7 +159,7 @@ tracerVendor(f::MDFFileV1)::Union{Vector{String}, Missing} = @keyrequired [f["/t
 tracerVendor(f::MDFFileV2)::Union{Vector{String}, Missing} = @keyrequired _makeStringArray(f["/tracer/vendor"])
 
 # scanner parameters
-scannerBoreSize(f::MDFFile)::Union{String, Nothing} = @keyoptional f["/scanner/boreSize"]
+scannerBoreSize(f::MDFFile)::Union{Float64, Nothing} = @keyoptional f["/scanner/boreSize"]
 scannerFacility(f::MDFFile)::Union{String, Missing} = @keyrequired f["/scanner/facility"]
 scannerOperator(f::MDFFile)::Union{String, Missing} = @keyrequired f["/scanner/operator"]
 scannerManufacturer(f::MDFFile)::Union{String, Missing} = @keyrequired f["/scanner/manufacturer"]

src/MDFInMemory.jl

@@ -660,27 +660,27 @@ function check(part::MDFv2Acquisition, variables::MDFv2Variables)
   # Check dimensions of `gradient` field
   if !isnothing(part.gradient)
     if isnothing(variables.J)
-      variables.J = size(part.gradient, 1)
+      variables.J = size(part.gradient, 4)
     else
-      @assert variables.J == size(part.gradient, 1) "Inconsistent dimension J in `gradient` in `acquisition`."
+      @assert variables.J == size(part.gradient, 4) "Inconsistent dimension J in `gradient` in `acquisition`."
     end
 
     if isnothing(variables.Y)
-      variables.Y = size(part.gradient, 2)
+      variables.Y = size(part.gradient, 3)
     else
-      @assert variables.Y == size(part.gradient, 1) "Inconsistent dimension Y in `gradient` in `acquisition`."
+      @assert variables.Y == size(part.gradient, 3) "Inconsistent dimension Y in `gradient` in `acquisition`."
     end
 
-    @assert size(part.gradient, 3) == 3 "Inconsistent third dimension in `gradient` in `acquisition`."
-    @assert size(part.gradient, 4) == 3 "Inconsistent fourth dimension in `gradient` in `acquisition`."
+    @assert size(part.gradient, 1) == 3 "Inconsistent first dimension in `gradient` in `acquisition`."
+    @assert size(part.gradient, 2) == 3 "Inconsistent second dimension in `gradient` in `acquisition`."
   end
 
   # Check dimensions of `offsetField` field
   if !isnothing(part.offsetField)
     if isnothing(variables.J)
-      variables.J = size(part.offsetField, 1)
+      variables.J = size(part.offsetField, 3)
     else
-      @assert variables.J == size(part.offsetField, 1) "Inconsistent dimension J in `offsetField` in `acquisition`."
+      @assert variables.J == size(part.offsetField, 3) "Inconsistent dimension J in `offsetField` in `acquisition`."
     end
 
     if isnothing(variables.Y)
@@ -689,7 +689,7 @@ function check(part::MDFv2Acquisition, variables::MDFv2Variables)
       @assert variables.Y == size(part.offsetField, 2) "Inconsistent dimension Y in `offsetField` in `acquisition`."
     end
 
-    @assert size(part.offsetField, 3) == 3 "Inconsistent third dimension in `offsetField` in `acquisition`."
+    @assert size(part.offsetField, 1) == 3 "Inconsistent first dimension in `offsetField` in `acquisition`."
   end
 end
 
@@ -699,26 +699,26 @@ function check(part::MDFv2Drivefield, variables::MDFv2Variables)
     variables.D = part.numChannels
   end
   if isnothing(variables.F)
-    variables.F = size(part.divider, 2)
+    variables.F = size(part.divider, 1)
   end
   if isnothing(variables.J)
-    variables.J = size(part.phase, 1)
+    variables.J = size(part.phase, 3)
   end
 
   # Then check dimensions for multidimensional fields
-  @assert variables.D == size(part.divider, 1) "Inconsistent dimension D in `divider` in `drivefield`."
-  @assert variables.F == size(part.divider, 2) "Inconsistent dimension F in `divider` in `drivefield`."
+  @assert variables.F == size(part.divider, 1) "Inconsistent dimension F in `divider` in `drivefield`."
+  @assert variables.D == size(part.divider, 2) "Inconsistent dimension D in `divider` in `drivefield`."
 
-  @assert variables.J == size(part.phase, 1) "Inconsistent dimension J in `phase` in `drivefield`."
+  @assert variables.F == size(part.phase, 1) "Inconsistent dimension F in `phase` in `drivefield`."
   @assert variables.D == size(part.phase, 2) "Inconsistent dimension D in `phase` in `drivefield`."
-  @assert variables.F == size(part.phase, 3) "Inconsistent dimension F in `phase` in `drivefield`."
+  @assert variables.J == size(part.phase, 3) "Inconsistent dimension J in `phase` in `drivefield`."
 
-  @assert variables.J == size(part.strength, 1) "Inconsistent dimension J in `strength` in `drivefield`."
+  @assert variables.F == size(part.strength, 1) "Inconsistent dimension F in `strength` in `drivefield`."
   @assert variables.D == size(part.strength, 2) "Inconsistent dimension D in `strength` in `drivefield`."
-  @assert variables.F == size(part.strength, 3) "Inconsistent dimension F in `strength` in `drivefield`."
+  @assert variables.J == size(part.strength, 3) "Inconsistent dimension J in `strength` in `drivefield`."
 
-  @assert variables.D == size(part.waveform, 1) "Inconsistent dimension D in `waveform` in `drivefield`."
-  @assert variables.F == size(part.waveform, 2) "Inconsistent dimension F in `waveform` in `drivefield`."
+  @assert variables.F == size(part.waveform, 1) "Inconsistent dimension F in `waveform` in `drivefield`."
+  @assert variables.D == size(part.waveform, 2) "Inconsistent dimension D in `waveform` in `drivefield`."
 end
 
 function check(part::MDFv2Receiver, variables::MDFv2Variables)
@@ -732,21 +732,21 @@ function check(part::MDFv2Receiver, variables::MDFv2Variables)
   end
 
   if !isnothing(part.dataConversionFactor)
-    @assert variables.C == size(part.dataConversionFactor, 1) "Inconsistent dimension C in `dataConversionFactor` in `receiver`."
-    @assert size(part.dataConversionFactor, 2) == 2 "Inconsistent second dimension in `dataConversionFactor` in `receiver`."
+    @assert variables.C == size(part.dataConversionFactor, 2) "Inconsistent dimension C in `dataConversionFactor` in `receiver`."
+    @assert size(part.dataConversionFactor, 1) == 2 "Inconsistent first dimension in `dataConversionFactor` in `receiver`."
   end
 
   if !isnothing(part.inductionFactor)
-    @assert variables.C == size(part.inductionFactor, 1) "Inconsistent dimension C in `inductionFactor` in `receiver`."
+    @assert variables.C == length(part.inductionFactor) "Inconsistent dimension C in `inductionFactor` in `receiver`."
   end
 
   if !isnothing(part.transferFunction)
-    @assert variables.C == size(part.transferFunction, 1) "Inconsistent dimension C in `transferFunction` in `receiver`."
+    @assert variables.C == size(part.transferFunction, 2) "Inconsistent dimension C in `transferFunction` in `receiver`."
 
     if isnothing(variables.K)
-      variables.K = size(part.transferFunction, 2)
+      variables.K = size(part.transferFunction, 1)
     else
-      @assert variables.K == size(part.transferFunction, 2) "Inconsistent dimension K in `transferFunction` in `receiver`."
+      @assert variables.K == size(part.transferFunction, 1) "Inconsistent dimension K in `transferFunction` in `receiver`."
     end
   end
 end
@@ -767,7 +767,7 @@ function check(part::MDFv2Measurement, variables::MDFv2Variables)
   if isnothing(variables.E)
     variables.E = length([x for x in part.isBackgroundFrame if x == true])
   end
-  # E is defined by the number of `false` values in isBackgroundFrame here; should have been retrieved earlier
+  # O is defined by the number of `false` values in isBackgroundFrame here; should have been retrieved earlier
   if isnothing(variables.O)
     variables.O = length([x for x in part.isBackgroundFrame if x == false])
   end
@@ -781,28 +781,28 @@ function check(part::MDFv2Measurement, variables::MDFv2Variables)
 
   if isnothing(variables.J)
     if !part.isSparsityTransformed
-      @warn "Can't determine variable J for measurement from `subsamplingIndices` since the dataset is not sparsity transformed."
+      @debug "Can't determine variable J for measurement from `subsamplingIndices` since the dataset is not sparsity transformed."
     else
       variables.J = size(part.subsamplingIndices, 1)
     end
   end
   if isnothing(variables.C)
     if !part.isSparsityTransformed
-      @warn "Can't determine variable C for measurement from `subsamplingIndices` since the dataset is not sparsity transformed. Should happen in receiver."
+      @debug "Can't determine variable C for measurement from `subsamplingIndices` since the dataset is not sparsity transformed. Should happen in receiver."
     else
       variables.C = size(part.subsamplingIndices, 2)
     end
   end
   if isnothing(variables.K)
     if !part.isSparsityTransformed
-      @warn "Can't determine variable K for measurement from `subsamplingIndices` since the dataset is not sparsity transformed. Should happen in receiver."
+      @debug "Can't determine variable K for measurement from `subsamplingIndices` since the dataset is not sparsity transformed. Should happen in receiver."
     else
       variables.K = size(part.subsamplingIndices, 3)
     end
   end
   if isnothing(variables.B)
     if !part.isSparsityTransformed
-      @warn "Can't determine variable B for measurement from `subsamplingIndices` since the dataset is not sparsity transformed. Should happen in receiver."
+      @debug "Can't determine variable B for measurement from `subsamplingIndices` since the dataset is not sparsity transformed. Should happen in receiver."
     else
       variables.B = size(part.subsamplingIndices, 4)
     end
@@ -829,10 +829,10 @@ function check(part::MDFv2Measurement, variables::MDFv2Variables)
 
   if part.isSparsityTransformed
     # J, C, K and B should be defined by now
-    @assert variables.J == size(part.subsamplingIndices, 1) "Inconsistent dimension J in `subsamplingIndices` in `measurement`."
-    @assert variables.C == size(part.subsamplingIndices, 2) "Inconsistent dimension C in `subsamplingIndices` in `measurement`."
-    @assert variables.K == size(part.subsamplingIndices, 3) "Inconsistent dimension K in `subsamplingIndices` in `measurement`."
-    @assert variables.B == size(part.subsamplingIndices, 4) "Inconsistent dimension B in `subsamplingIndices` in `measurement`."
+    @assert variables.B == size(part.subsamplingIndices, 1) "Inconsistent dimension B in `subsamplingIndices` in `measurement`."
+    @assert variables.K == size(part.subsamplingIndices, 2) "Inconsistent dimension K in `subsamplingIndices` in `measurement`."
+    @assert variables.C == size(part.subsamplingIndices, 3) "Inconsistent dimension C in `subsamplingIndices` in `measurement`."
+    @assert variables.J == size(part.subsamplingIndices, 4) "Inconsistent dimension J in `subsamplingIndices` in `measurement`."
   end
 end
 
@@ -851,11 +851,11 @@ function check(part::MDFv2Calibration, variables::MDFv2Variables)
 
   if !isnothing(part.offsetFields)
     if isnothing(variables.O)
-      variables.O = size(part.offsetFields, 1)
+      variables.O = size(part.offsetFields, 2)
     else
-      @assert variables.O == size(part.offsetFields, 1) "Inconsistent dimension O in `offsetFields` in `calibration`."
+      @assert variables.O == size(part.offsetFields, 2) "Inconsistent dimension O in `offsetFields` in `calibration`."
     end
-    @assert size(part.offsetFields, 2) == 3 "Inconsistent second dimension in `offsetFields` in `calibration`."
+    @assert size(part.offsetFields, 1) == 3 "Inconsistent first dimension in `offsetFields` in `calibration`."
   end
 
   if !isnothing(part.order)
@@ -864,8 +864,8 @@ function check(part::MDFv2Calibration, variables::MDFv2Variables)
 
   if !isnothing(part.positions)
     # O must be defined by now
-    @assert variables.O == size(part.positions, 1) "Inconsistent dimension O in `positions` in `calibration`."
-    @assert size(part.positions, 2) == 3 "Inconsistent second dimension in `positions` in `calibration`."
+    @assert variables.O == size(part.positions, 2) "Inconsistent dimension O in `positions` in `calibration`."
+    @assert size(part.positions, 1) == 3 "Inconsistent first dimension in `positions` in `calibration`."
   end
 
   if !isnothing(part.size)
@@ -876,9 +876,9 @@ function check(part::MDFv2Calibration, variables::MDFv2Variables)
 
   if !isnothing(part.snr)
     if isnothing(variables.J)
-      variables.J = size(part.snr, 1)
+      variables.J = size(part.snr, 3)
     else
-      @assert variables.J == size(part.snr, 1) "Inconsistent dimension J in `snr` in `calibration`."
+      @assert variables.J == size(part.snr, 3) "Inconsistent dimension J in `snr` in `calibration`."
     end
 
     if isnothing(variables.C)
@@ -888,17 +888,17 @@ function check(part::MDFv2Calibration, variables::MDFv2Variables)
     end
 
     if isnothing(variables.K)
-      variables.K = size(part.snr, 3)
+      variables.K = size(part.snr, 1)
     else
-      @assert variables.K == size(part.snr, 3) "Inconsistent dimension K in `snr` in `calibration`."
+      @assert variables.K == size(part.snr, 1) "Inconsistent dimension K in `snr` in `calibration`."
     end
   end
 end
 
 function check(part::MDFv2Reconstruction, variables::MDFv2Variables)
   # Pick variables first
   if isnothing(variables.Q)
-    variables.Q = size(part.data, 1)
+    variables.Q = size(part.data, 3)
   end
   if isnothing(variables.P)
     variables.P = size(part.data, 2)
@@ -924,8 +924,8 @@ function check(part::MDFv2Reconstruction, variables::MDFv2Variables)
   end
 
   if !isnothing(part.positions)
-    @assert variables.P == size(part.positions, 1) "Inconsistent dimension P in `positions` in `reconstruction`."
-    @assert size(part.positions, 2) == 3 "Inconsistent second dimension in `positions` in `reconstruction`."
+    @assert variables.P == size(part.positions, 2) "Inconsistent dimension P in `positions` in `reconstruction`."
+    @assert size(part.positions, 1) == 3 "Inconsistent first dimension in `positions` in `reconstruction`."
   end
 
   if !isnothing(part.size)
@@ -1382,7 +1382,7 @@ function inMemoryMDFFromMDFFileV2(mdfFile::MDFFileV2)::MDFv2InMemory
     try
       result = f(mdfFile)
     catch e
-      @warn "Exception while reading symbol $(functionSymbol). Please check closely."
+      @warn "Exception while reading symbol $(functionSymbol). Please check closely. Exception was `$e`."
     end
 
     if !(isnothing(result) || ismissing(result))

src/MPIFiles.jl

@@ -59,8 +59,8 @@ export tracerName, tracerBatch, tracerVolume, tracerConcentration,
   tracerSolute, tracerInjectionTime, tracerVendor
 
 # scanner parameters
-export scannerFacility, scannerOperator, scannerManufacturer, scannerName,
-  scannerTopology
+export scannerBoreSize, scannerFacility, scannerOperator, scannerManufacturer,
+   scannerName, scannerTopology
 
 # acquisition parameters
 export acqStartTime, acqNumFrames, acqNumAverages,

src/Measurements.jl

@@ -321,7 +321,7 @@ Supported keyword arguments:
 """
 function getMeasurementsFD(f::MPIFile, args...;
       loadasreal=false, transposed=false, frequencies=nothing,
-      tfCorrection=rxHasTransferFunction(f),  kargs...)
+      tfCorrection=rxHasTransferFunction(f), kargs...)
 
   data = getMeasurements(f, args..., tfCorrection=false; kargs...)
 
@@ -354,13 +354,13 @@ function getMeasurementsFD(f::MPIFile, args...;
     end
   end
 
-  if frequencies != nothing
+  if !isnothing(frequencies)
     # here we merge frequencies and channels
     data = data[frequencies, :, :]
   end
 
   if transposed
-    if frequencies != nothing
+    if !isnothing(frequencies)
       data = permutedims(data, [3,1,2])
     else
       data = permutedims(data, [4,1,2,3])
@@ -374,12 +374,6 @@ function getMeasurementsFD(f::MPIFile, args...;
   return data
 end
 
-
-
-
-
-
-
 function spectralLeakageCorrectedData(dataIn)
   @debug "Apply Spectral Cleaning"