Changes to get the IMT Bruker system running

src/Brukerfile.jl

@@ -84,7 +84,7 @@ function BrukerFile(path::String; isCalib=_iscalib(path), fastMode=false,
 				 "PVM_MPI_NrCalibrationScans","MPI_NSteps",
                                  "PVM_MPI_NrBackgroundMeasurementCalibrationAllScans",
 				 "PVM_MPI_NrBackgroundMeasurementCalibrationAdditionalScans",
-				 "PVM_MPI_ChannelSelect", "PVM_MPI_Tracer", "PVM_MPI_DriveFieldCycle", "PVM_Matrix", "PVM_Fov"]   
+				 "PVM_MPI_ChannelSelect", "PVM_MPI_Tracer", "PVM_MPI_DriveFieldCycle", "PVM_Matrix", "PVM_Fov", "PVM_MPI_FovCenter"]   
   else
     maxEntriesAcqp = 2000
 	  keylistAcqp = String[]
@@ -433,20 +433,22 @@ function measData(b::BrukerFileMeas, frames=1:acqNumFrames(b), periods=1:acqNumP
   if numSubPeriods(b) == 1
     raw = Mmap.mmap(s, Array{dType,4},
              (rxNumSamplingPoints(b),rxNumChannels(b),acqNumPeriodsPerFrame(b),acqNumFrames(b)))
+    data = raw[:,receivers,periods,frames]
   else
     if b.handleSubPeriodsAsFrames
       raw = Mmap.mmap(s, Array{dType,5}, (rxNumSamplingPoints(b),numSubPeriods(b),rxNumChannels(b),
                          acqNumPeriodsPerFrame(b), div(acqNumFrames(b),numSubPeriods(b))))
 
       raw = reshape(permutedims(collect(raw), (1,3,4,2,5)), Val(4))
+      data = raw[:,receivers,periods,frames]
     else 
       raw = Mmap.mmap(s, Array{dType,5},
       (rxNumSamplingPoints(b),numSubPeriods(b),rxNumChannels(b),acqNumPeriodsPerFrame(b),acqNumFrames(b)))
 
-      raw = dropdims(sum(raw,dims=2),dims=2)
+      data = dropdims(sum(raw[:,:,receivers,periods,frames],dims=2),dims=2)
     end
   end
-  data = raw[:,receivers,periods,frames]
+
   close(s)
 
   return reshape(data, rxNumSamplingPoints(b), length(receivers),length(periods),length(frames))
@@ -770,5 +772,4 @@ function getBV(b; recChannels=1:rxNumChannels(b))
   data = Mmap.mmap(s, Array{Float64,2}, (nFreq,rxNumChannels(b)))
   close(s)
   return data
-end
-
+end

src/Conversion.jl

@@ -160,9 +160,9 @@ end
 
 function appendBGDataset(params::Dict, fBG::MPIFile; frames=1:acqNumFrames(fBG))
   paramsBG = loadDataset(fBG, frames=frames)
-  paramsBG[:measIsBGFrame][:] = true
+  paramsBG[:measIsBGFrame][:] .= true
 
-  params[:measData] = cat(4, params[:measData], paramsBG[:measData])
+  params[:measData] = cat(params[:measData], paramsBG[:measData], dims=4)
   params[:measIsBGFrame] = cat(params[:measIsBGFrame], paramsBG[:measIsBGFrame], dims=1)
   params[:acqNumFrames] += paramsBG[:acqNumFrames]
 
@@ -838,6 +838,9 @@ function saveasMDF(file::HDF5.File, params::Dict{Symbol,Any})
       write(file, "/reconstruction/positions", params[:recoPositions])
     end
     if hasKeyAndValue(params, :recoParameters)
+      ## Workaround to save new parameters to MDF, maybe not the best way to do it...
+      params[:recoParameters][:solver] = string(params[:recoParameters][:solver])
+      params[:recoParameters][:reg] = string(params[:recoParameters][:reg])
       saveParams(file, "/reconstruction/_parameters", params[:recoParameters])
     end
   end

src/DatasetStore/BrukerDatasetStore.jl

@@ -2,8 +2,11 @@ export BrukerDatasetStore, findBrukerFiles, getNewCalibNum
 
 struct BrukerDatasetStore <: DatasetStore
   path::String
+  readonly::Bool
 end
 
+BrukerDatasetStore(path::String) = BrukerDatasetStore(path, true)
+
 @static if ispath("/opt/mpidata")
   export BrukerStore
   const BrukerStore = BrukerDatasetStore("/opt/mpidata")
@@ -15,7 +18,7 @@ iscalib(e::Experiment{BrukerDatasetStore}) = _iscalib(path(e))
 
 ###  Implementations of abstract interfaces ###
 
-readonly(::BrukerDatasetStore) = true
+readonly(d::BrukerDatasetStore) = d.readonly
 
 studydir(d::BrukerDatasetStore) = d.path
 calibdir(d::BrukerDatasetStore) = error("BrukerDatasetStore has no calibdir")
@@ -81,7 +84,7 @@ function getExperiments(s::Study{BrukerDatasetStore})
   end
 
   experiments = Experiment[]
-
+  
   for file in files
     prefix, ext = splitext(splitpath(file)[end])
     num = tryparse(Int64, prefix)

src/DatasetStore/SFDatabase.jl

@@ -16,11 +16,13 @@ function findSFFiles(d::BrukerDatasetStore)
       end
     end
   end
-  BrukerMDFSFs = readdir("/opt/data/MDF_SFs/")
-  for BrukerMDFSF in BrukerMDFSFs
-    prefix, ext = splitext(BrukerMDFSF)
-     if ext == ".mdf"
-      push!(bfiles,joinpath("/opt/data/MDF_SFs/",BrukerMDFSF))
+  if isdir("/opt/data/MDF_SFs/")
+    BrukerMDFSFs = readdir("/opt/data/MDF_SFs/")
+    for BrukerMDFSF in BrukerMDFSFs
+      prefix, ext = splitext(BrukerMDFSF)
+      if ext == ".mdf"
+        push!(bfiles,joinpath("/opt/data/MDF_SFs/",BrukerMDFSF))
+      end
     end
   end
   return bfiles
@@ -130,8 +132,13 @@ end
 
 # HAAACKKK
 function generateSFDatabase(d::BrukerDatasetStore)
-  oldfile = "/opt/data/SF_DatabaseOld.csv"
-  newfile = "/opt/data/SF_Database.csv"
+  if readonly(d)
+    dbpath = "/opt/data"
+  else
+    dbpath = d.path
+  end
+  oldfile = joinpath(dbpath, "SF_DatabaseOld.csv")
+  newfile = joinpath(dbpath, "SF_Database.csv")
   generateSFDatabase_(d, oldfile, newfile)
 end
 
@@ -149,10 +156,16 @@ function generateSFDatabase_(d::DatasetStore, oldfile, newfile)
 end
 
 function loadSFDatabase(d::BrukerDatasetStore)
-  if isfile("/opt/data/SF_Database.csv")
-    A = readdlm("/opt/data/SF_Database.csv",',')
+  if readonly(d)
+    dbpath = "/opt/data"
+  else
+    dbpath = d.path
+  end
+  filepath = joinpath(dbpath, "SF_Database.csv")
+  if isfile(filepath)
+    A = readdlm(filepath,',')
     if size(A,2) < 16
-      A = readdlm("/opt/data/SF_Database.csv",'\t')
+      A = readdlm(filepath,'\t')
     end
     return A
   else