Change getindex to return KeyError (#62)

* Change `getindex` to return KeyErrror

* Fix errors with missing induction factor

* Some checks

* Fix stupid logic mistake

* Remove warning

* Fix tests

src/Conversion.jl

@@ -4,18 +4,18 @@ export getFFdataPerPos, prepareAsMDFSingleMeasurement, convertCustomSF, blockAve
 
 
 function setparam!(params::Dict, parameter, value)
-  if value != nothing
+  if !(isnothing(value) || ismissing(value))
     params[parameter] = value
   end
 end
 
 # we do not support all conversion possibilities
 function loadDataset(f::MPIFile; frames=1:acqNumFrames(f), applyCalibPostprocessing=false,
-                     numPeriodAverages=1, numPeriodGrouping=1, experimentNumber=nothing,
+                     numPeriodAverages=1, numPeriodGrouping=1, experimentNumber=missing,
                      fixDistortions=false, kargs...)
   params = loadMetadata(f)
 
-  if experimentNumber != nothing
+  if !ismissing(experimentNumber)
     params[:experimentNumber] = experimentNumber
   end
 
@@ -63,7 +63,7 @@ function loadDataset(f::MPIFile; frames=1:acqNumFrames(f), applyCalibPostprocess
           cat(zeros(Bool,acqNumFGFrames(f)),ones(Bool,acqNumBGFrames(f)), dims=1))
 
         snr = calibSNR(f)
-	      if snr == nothing
+	      if isnothing(snr)
           @info "calculate SNR"
           snr = calculateSystemMatrixSNR(f, data, numPeriodAverages=numPeriodAverages, numPeriodGrouping=numPeriodGrouping)
         end
@@ -151,8 +151,6 @@ function loadMeasParams(f, params = Dict{Symbol,Any}(); skipMeasData = false)
   return params
 end
 
-
-
 function appendBGDataset(params::Dict, filenameBG::String; kargs...)
   params = MPIFile(filenameBG) do fBG 
     appendBGDataset(params, fBG; kargs...)
@@ -171,7 +169,6 @@ function appendBGDataset(params::Dict, fBG::MPIFile; frames=1:acqNumFrames(fBG))
   return params
 end
 
-
 isConvertibleToMDF(f::MPIFile) = true
 function isConvertibleToMDF(f::BrukerFile)
   # check if raw data is consistent
@@ -196,16 +193,15 @@ function saveasMDF(filenameOut::String, filenameIn::String; kargs...)
 end
 
 function saveasMDF(filenameOut::String, f::MPIFile; filenameBG = nothing, enforceConversion=false, kargs...)
-
   # This is a hack. Needs to be fixed properly
-  if(haskey(kargs, :SNRThresh) || haskey(kargs, :sparsityTrafoRedFactor)) && calibSNR(f) != nothing
+  if(haskey(kargs, :SNRThresh) || haskey(kargs, :sparsityTrafoRedFactor)) && !isnothing(calibSNR(f))
     compressCalibMDF(filenameOut, f; kargs...)
     return
   end
 
   if enforceConversion || isConvertibleToMDF(f)
-    params = loadDataset(f;kargs...)
-    if filenameBG != nothing
+    params = loadDataset(f; kargs...)
+    if !isnothing(filenameBG)
       appendBGDataset(params, filenameBG)
     end
     saveasMDF(filenameOut, params)
@@ -746,7 +742,7 @@ function saveasMDF(file::HDF5.File, params::Dict{Symbol,Any})
   write(file, "/scanner/topology", get(params,:scannerTopology,"FFP"))
 
   # acquisition parameters
-  write(file, "/acquisition/numAverages",  params[:acqNumAverages])
+  write(file, "/acquisition/numAverages", params[:acqNumAverages])
   write(file, "/acquisition/numFrames", get(params,:acqNumFrames,1))
   write(file, "/acquisition/numPeriodsPerFrame", get(params,:acqNumPeriodsPerFrame,1))
   write(file, "/acquisition/startTime", "$( get(params,:acqStartTime, Dates.unix2datetime(time())) )")

src/MDF.jl

@@ -69,13 +69,7 @@ function h5haskey(filename, parameter)
   end
 end
 
-function getindex(f::MDFFile, parameter)
-  if haskey(f.file, parameter)
-    return read(f.file, parameter)
-  else
-    return nothing
-  end
-end
+getindex(f::MDFFile, parameter) = read(f.file, parameter)
 
 function getindex(f::MDFFile, parameter, default)
   #if !haskey(f.param_cache,parameter)
@@ -106,8 +100,8 @@ studyUuid(f::MDFFileV2) = @keyrequired UUID(f["/study/uuid"])
 studyDescription(f::MDFFileV1)::Union{String, Missing} = "n.a."
 studyDescription(f::MDFFileV2)::Union{String, Missing} = @keyrequired f["/study/description"]
 function studyTime(f::MDFFile)
-  t = f["/study/time"]
-  if typeof(t)==String
+  t = @keyoptional f["/study/time"]
+  if typeof(t) == String
    return DateTime(t)
   else
    return nothing

src/MDFInMemory.jl

@@ -1407,7 +1407,11 @@ function inMemoryMDFFromMDFFileV2(mdfFile::MDFFileV2)::MDFv2InMemory
   end
 
   # Add measurements data
-  measDataRaw(mdf, mdfFile.mmap_measData)
+  if !isnothing(mdfFile.mmap_measData)
+    measDataRaw(mdf, mdfFile.mmap_measData)
+  else
+    @warn "The measurement data could not be read. Please check closely."
+  end
 
   return mdf
 end
@@ -1477,7 +1481,6 @@ measObservedDriveField(mdf::MDFv2InMemory, measDriveFields) = mdf.custom["measOb
 measAppliedDriveField(mdf::MDFv2InMemory) = @keyoptional mdf.custom["measAppliedDriveField"]
 measAppliedDriveField(mdf::MDFv2InMemory, measTransmit) = mdf.custom["measAppliedDriveField"] = measTransmit
 
-
 auxiliaryData(mdf::MDFv2InMemory) = @keyoptional mdf.custom["auxiliaryData"]
 auxiliaryData(mdf::MDFv2InMemory, auxiliaryData) = mdf.custom["auxiliaryData"] = auxiliaryData
 

src/Measurements.jl

@@ -268,6 +268,10 @@ function getMeasurements(f::MPIFile, neglectBGFrames=true;
   if tfCorrection && !measIsTFCorrected(f)
     tf = rxTransferFunction(f)
     inductionFactor = rxInductionFactor(f)
+    if ismissing(inductionFactor)
+      @warn "The file is missing the induction factor. The induction factor will be set to 1."
+      inductionFactor = ones(Float64, rxNumChannels(f))
+    end
 
     J = size(data,1)
     dataF = rfft(data, 1)
@@ -323,6 +327,11 @@ function getMeasurementsFD(f::MPIFile, args...;
   if tfCorrection && !measIsTFCorrected(f)
     tf = rxTransferFunction(f)
     inductionFactor = rxInductionFactor(f)
+    if ismissing(inductionFactor)
+      @warn "The file is missing the induction factor. The induction factor will be set to 1."
+      inductionFactor = ones(Float64, rxNumChannels(f))
+    end
+
     data[2:end,:,:,:] ./= tf[2:end,:,:,:]
 
     if all(tf[1,:,:,:] .!= 0) && !any(isnan.(tf[1,:,:,:]))