progress

Author: tknopp

examples/reco3D.jl

@@ -1,34 +1,37 @@
-using OpenMPIData
+using PyPlot, MPIReco, OpenMPIData
 
-filenameCalib = Pkg.dir("OpenMPIData","data","calibrations","3.mdf")
-#filenameCalib = Pkg.dir("OpenMPIData","data","calibrations","6.mdf")#High Resolution
+include("visualization.jl")
+
+filenameCalib = joinpath(OpenMPIData.basedir(),"data","calibrations","3.mdf")
+#filenameCalib = joinpath(OpenMPIData.basedir(),"data","calibrations","6.mdf")#High Resolution
 
 ### Shape Phantom
- phantom = "shapePhantom"
+# phantom = "shapePhantom"
 ### Resolution Phantom
 # phantom = "resolutionPhantom"
 ### Concentration Phantom
-# phantom = "concentrationPhantom"
+ phantom = "concentrationPhantom"
+
+filenameMeas = joinpath(OpenMPIData.basedir(),"data","measurements",phantom,"3.mdf")
 
-filenameMeas = Pkg.dir("OpenMPIData","data","measurements",phantom,"3.mdf")
 
+c = reconstruction(filenameCalib, filenameMeas, iterations=3, lambd=0.001, bgCorrectionInternal=false,
+                   minFreq=80e3, SNRThresh=2.0, recChannels=1:3, frames=1:1000, nAverages=1000)
 
-c = reconstruction(filenameCalib, filenameMeas, iterations=3, lambda=0.001,
-                   minFreq=80e3, SNRThresh=2.0, recChannels=1:3)
-mkpath( Pkg.dir("OpenMPIData","data/reconstructions/$(phantom)"))
-s=size(c)
+mkpath( joinpath(OpenMPIData.basedir(),"data/reconstructions/$(phantom)"))
+s=size(c)[2:4]
 if phantom =="shapePhantom"
-  filenameImage = Pkg.dir("OpenMPIData","data","reconstructions","$phantom","reconstruction3D.png")
-  showMIPs(c[:,:,:,1],filename=filenameImage)
+  filenameImage = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction3D.png")
+  showMIPs(c[1,:,:,:,1],filename=filenameImage)
 elseif phantom =="resolutionPhantom"
   slice=[div(s[1]+1,2),div(s[2]+1,2),div(s[3]+1,2)]
-  filenameImage = Pkg.dir("OpenMPIData","data","reconstructions","$phantom","reconstruction3D.png")
-  showSlices(c[:,:,:,1],slice,filename=filenameImage)
+  filenameImage = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction3D.png")
+  showSlices(c[1,:,:,:,1],slice,filename=filenameImage)
 elseif phantom =="concentrationPhantom"
   slice1=[div(s[1],3)+1,div(s[2],3)+1,div(s[3],3)+1]
   slice2=[2*div(s[1],3)+1,2*div(s[2],3)+1,2*div(s[3],3)+1]
-  filenameImage = Pkg.dir("OpenMPIData","data","reconstructions","$phantom","reconstruction3D_1.png")
-  showSlices(c[:,:,:,1],slice1,filename=filenameImage,fignum=1)
-  filenameImage = Pkg.dir("OpenMPIData","data","reconstructions","$phantom","reconstruction3D_2.png")
-  showSlices(c[:,:,:,1],slice2,filename=filenameImage,fignum=2)
+  filenameImage = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction3D_1.png")
+  showSlices(c[1,:,:,:,1],slice1,filename=filenameImage,fignum=1)
+  filenameImage = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction3D_2.png")
+  showSlices(c[1,:,:,:,1],slice2,filename=filenameImage,fignum=2)
 end

src/visualization.jl examples/visualization.jl

@@ -1,11 +1,11 @@
-export showMIPs,showSlices
+export showMIPs, showSlices
 
 
-function showMIPs(c::Array; fignum=1, filename=nothing)
-  cAbs = abs.(c)
-  cxy = maximum(cAbs,3)[:,:,1]
-  cxz = maximum(cAbs,2)[:,1,:]
-  cyz = maximum(cAbs,1)[1,:,:]
+function showMIPs(c; fignum=1, filename=nothing)
+  cAbs = abs.(data(c))
+  cxy = maximum(cAbs,dims=3)[:,:,1]
+  cxz = maximum(cAbs,dims=2)[:,1,:]
+  cyz = maximum(cAbs,dims=1)[1,:,:]
 
   figure(fignum, figsize=(4,4))
 
@@ -25,8 +25,8 @@ function showMIPs(c::Array; fignum=1, filename=nothing)
     savefig(filename)
   end
 end
-function showSlices(c::Array,slice; fignum=1, filename=nothing)
-  cAbs = abs.(c)
+function showSlices(c, slice; fignum=1, filename=nothing)
+  cAbs = abs.(data(c))
   x=slice[1]
   y=slice[2]
   z=slice[3]

src/OpenMPIData.jl

@@ -1,11 +1,7 @@
 module OpenMPIData
 
 using Reexport
-@reexport using MPIFiles
-#@reexport using PyPlot
 
 include("download.jl")
-include("reconstruction.jl")
-#include("visualization.jl")
 
 end # module