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Add GPU reconstruction example #14

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a8b7138
Update MPIReco API and move to CairoMakie for plotting
nHackel Jul 12, 2024
84c4c25
Init example for GPU reco (no good pictures yet)
nHackel Jul 12, 2024
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14 changes: 8 additions & 6 deletions examples/reco1D.jl
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Original file line number Diff line number Diff line change
@@ -1,16 +1,18 @@
using PyPlot, MPIReco, OpenMPIData
using CairoMakie, MPIReco, OpenMPIData, MPIReco.RegularizedLeastSquares

include("visualization.jl")

filenameCalib = joinpath(OpenMPIData.basedir(),"data","calibrations","1.mdf")
#filenameCalib = joinpath(OpenMPIData.basedir(),"data","calibrations","4.mdf")
calib = MPIFile(filenameCalib)

for (i,phantom) in enumerate(["shapePhantom", "resolutionPhantom", "concentrationPhantom"])

filenameMeas = joinpath(OpenMPIData.basedir(),"data","measurements",phantom,"1.mdf")
meas = MPIFile(filenameMeas)

# reconstruct data
c = reconstruction(filenameCalib, filenameMeas, iterations=10, lambd=0.001,
c = reconstruct("SinglePatch", meas; sf = calib, iterations=10, reg= [L2Regularization(0.001)], solver = Kaczmarz,
minFreq=80e3, SNRThresh=1.25, recChannels=1:3,
bgCorrectionInternal=true, spectralLeakageCorrection=false)[:,:,10:28,10:28,:]

Expand All @@ -20,18 +22,18 @@ for (i,phantom) in enumerate(["shapePhantom", "resolutionPhantom", "concentratio
# visualization
if phantom =="shapePhantom"
filenameImage = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction1D.png")
showMIPs(c[1,:,:,:,1],filename=filenameImage, fignum=i)
showMIPs(c[1,:,:,:,1],filename=filenameImage)
elseif phantom =="resolutionPhantom"
slice=[div(s[1]+1,2),div(s[2]+1,2),div(s[3]+1,2)]
filenameImage = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction1D.png")
showSlices(c[1,:,:,:,1],slice,filename=filenameImage, fignum=i)
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,div(s[3],3)+1]
filenameImage = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction1D_1.png")
showSlices(c[1,:,:,:,1],slice1,filename=filenameImage,fignum=i)
showSlices(c[1,:,:,:,1],slice1,filename=filenameImage)
filenameImage = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction1D_2.png")
showSlices(c[1,:,:,:,1],slice2,filename=filenameImage,fignum=i+1)
showSlices(c[1,:,:,:,1],slice2,filename=filenameImage)
end
end

Expand Down
14 changes: 8 additions & 6 deletions examples/reco2D.jl
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Original file line number Diff line number Diff line change
@@ -1,16 +1,18 @@
using PyPlot, MPIReco, OpenMPIData
using CairoMakie, MPIReco, OpenMPIData

include("visualization.jl")

filenameCalib = joinpath(OpenMPIData.basedir(),"data","calibrations","2.mdf")
#filenameCalib = joinpath(OpenMPIData.basedir(),"data","calibrations","5.mdf")
calib = MPIFile(filenameCalib)

for (i,phantom) in enumerate(["shapePhantom", "resolutionPhantom", "concentrationPhantom"])

filenameMeas = joinpath(OpenMPIData.basedir(),"data","measurements",phantom,"2.mdf")
meas = MPIFile(filenameMeas)

# reconstruct data
c = reconstruction(filenameCalib, filenameMeas, iterations=10, lambd=0.01,
c = reconstruct("SinglePatch", meas; sf = calib, iterations=10, reg= [L2Regularization(0.01)], solver = Kaczmarz,
minFreq=80e3, SNRThresh=1.5, recChannels=1:3,
bgCorrectionInternal=true, spectralLeakageCorrection=false)[:,:,:,10:28,:]

Expand All @@ -20,17 +22,17 @@ for (i,phantom) in enumerate(["shapePhantom", "resolutionPhantom", "concentratio
# visualization
if phantom =="shapePhantom"
filenameImage = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction2D.png")
showMIPs(c[1,:,:,:,1],filename=filenameImage, fignum=i)
showMIPs(c[1,:,:,:,1],filename=filenameImage)
elseif phantom =="resolutionPhantom"
slice=[div(s[1]+1,2),div(s[2]+1,2),div(s[3]+1,2)]
filenameImage = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction2D.png")
showSlices(c[1,:,:,:,1],slice,filename=filenameImage, fignum=i)
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,div(s[3],3)+1]
filenameImage = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction2D_1.png")
showSlices(c[1,:,:,:,1],slice1,filename=filenameImage,fignum=i)
showSlices(c[1,:,:,:,1],slice1,filename=filenameImage)
filenameImage = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction2D_2.png")
showSlices(c[1,:,:,:,1],slice2,filename=filenameImage,fignum=i+1)
showSlices(c[1,:,:,:,1],slice2,filename=filenameImage)
end
end
17 changes: 10 additions & 7 deletions examples/reco3D.jl
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Original file line number Diff line number Diff line change
@@ -1,36 +1,39 @@
using PyPlot, MPIReco, OpenMPIData
using CairoMakie, MPIReco, OpenMPIData, MPIReco.RegularizedLeastSquares

include("visualization.jl")

filenameCalib = joinpath(OpenMPIData.basedir(),"data","calibrations","3.mdf")
#filenameCalib = joinpath(OpenMPIData.basedir(),"data","calibrations","6.mdf")#High Resolution
calib = MPIFile(filenameCalib)


for (i,phantom) in enumerate(["shapePhantom", "resolutionPhantom", "concentrationPhantom"])

filenameMeas = joinpath(OpenMPIData.basedir(),"data","measurements",phantom,"3.mdf")
meas = MPIFile(filenameMeas)

# reconstruct data
c = reconstruction(filenameCalib, filenameMeas, iterations=3, lambd=0.001, bgCorrectionInternal=false,
minFreq=80e3, SNRThresh=2.0, recChannels=1:3, frames=1:1000, numAverages=1000)
c = reconstruct("SinglePatch", meas; sf = calib, iterations=3, reg= [L2Regularization(0.001)], bgCorrectionInternal=false,
minFreq=80e3, SNRThresh=2.0, recChannels=1:3, frames=1:1000, numAverages=1000, solver = Kaczmarz)

mkpath( joinpath(OpenMPIData.basedir(),"data/reconstructions/$(phantom)"))
s = size(c)[2:4]

# visualization
if phantom =="shapePhantom"
filenameImage = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction3D.png")
showMIPs(c[1,:,:,:,1],filename=filenameImage,fignum=i)
showMIPs(c[1,:,:,:,1],filename=filenameImage)
elseif phantom =="resolutionPhantom"
slice=[div(s[1]+1,2),div(s[2]+1,2),div(s[3]+1,2)]
filenameImage = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction3D.png")
showSlices(c[1,:,:,:,1],slice,filename=filenameImage, fignum=i)
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 = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction3D_1.png")
showSlices(c[1,:,:,:,1],slice1,filename=filenameImage,fignum=i)
showSlices(c[1,:,:,:,1],slice1,filename=filenameImage)
filenameImage = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction3D_2.png")
showSlices(c[1,:,:,:,1],slice2,filename=filenameImage,fignum=i+1)
showSlices(c[1,:,:,:,1],slice2,filename=filenameImage)
end

end
46 changes: 46 additions & 0 deletions examples/reco3D_gpu.jl
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Original file line number Diff line number Diff line change
@@ -0,0 +1,46 @@
using CairoMakie, MPIReco, OpenMPIData, MPIReco.RegularizedLeastSquares

# Add GPU package
using CUDA # or AMDGPU, Metal, ...
arrayType = CuArray # or ROCArray, ....


include("visualization.jl")

filenameCalib = joinpath(OpenMPIData.basedir(),"data","calibrations","3.mdf")
#filenameCalib = joinpath(OpenMPIData.basedir(),"data","calibrations","6.mdf")#High Resolution
calib = MPIFile(filenameCalib)


for (i,phantom) in enumerate(["shapePhantom"]) # , "resolutionPhantom", "concentrationPhantom"])

filenameMeas = joinpath(OpenMPIData.basedir(),"data","measurements",phantom,"3.mdf")
meas = MPIFile(filenameMeas)

# reconstruct data
c = reconstruct("SinglePatch", meas; sf = calib, iterations=300, reg= [L2Regularization(0.1)], rho = 0.95, bgCorrectionInternal=false,
minFreq=80e3, SNRThresh=2.0, recChannels=1:3, frames=1:1000, numAverages=1000,
solver = CGNR, # Kaczmarz is not well suited for GPU recos
arrayType = arrayType) # Specify arraytype for GPU reconstruction

mkpath( joinpath(OpenMPIData.basedir(),"data/reconstructions/$(phantom)"))
s = size(c)[2:4]

# visualization
if phantom =="shapePhantom"
filenameImage = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction3D_$(parentmodule(arrayType)).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 = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction3D_$(parentmodule(arrayType)).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 = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction3D_1_$(parentmodule(arrayType)).png")
showSlices(c[1,:,:,:,1],slice1,filename=filenameImage)
filenameImage = joinpath(OpenMPIData.basedir(),"data","reconstructions","$phantom","reconstruction3D_2_$(parentmodule(arrayType)).png")
showSlices(c[1,:,:,:,1],slice2,filename=filenameImage)
end

end
56 changes: 24 additions & 32 deletions examples/visualization.jl
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Original file line number Diff line number Diff line change
@@ -1,33 +1,29 @@
export showMIPs, showSlices

PyPlot.rc("font", family="serif")
PyPlot.rc("text", usetex=true)
Makie.update_theme!(fonts = (regular = Makie.texfont(), bold = Makie.texfont(:bold), italic = Makie.texfont(:italic)))

function showMIPs(c; fignum=1, filename=nothing)
function showMIPs(c;filename=nothing)
cAbs = abs.(arraydata(c))
cxy = maximum(cAbs,dims=3)[:,:,1]
cxz = maximum(cAbs,dims=2)[:,1,:]
cyz = maximum(cAbs,dims=1)[1,:,:]

figure(fignum, figsize=(4,4))

subplot(2,2,1)
imshow(cxz', interpolation="nearest")
title("MIP xz")
subplot(2,2,2)
imshow(cyz', interpolation="nearest")
title("MIP yz")
subplot(2,2,4)
imshow(cxy, interpolation="nearest")
title("MIP xy")

subplots_adjust(wspace=0.18,hspace=0.3,left=0.06,bottom=0.06,right=1.0,top=0.93)
fig = Figure()
g = GridLayout(fig[1,1])
ax = CairoMakie.Axis(g[1,1], title = "MIP xz", width = 150, height = 150)
heatmap!(ax, cxz)
ax = CairoMakie.Axis(g[1,2], title = "MIP yz", width = 150, height = 150 )
heatmap!(ax, cyz)
ax = CairoMakie.Axis(g[2,2], title = "MIP xy", width = 150, height = 150)
heatmap!(ax, cxy)

resize_to_layout!(fig)
if filename != nothing
savefig(filename)
save(filename, fig)
end
end
function showSlices(c, slice; fignum=1, filename=nothing)

function showSlices(c, slice;filename=nothing)
cAbs = abs.(arraydata(c))
x=slice[1]
y=slice[2]
Expand All @@ -37,21 +33,17 @@ function showSlices(c, slice; fignum=1, filename=nothing)
cxz = cAbs[:,y,:]
cyz = cAbs[x,:,:]

figure(fignum, figsize=(4,4))

subplot(2,2,1)
imshow(cxz', interpolation="nearest")
title("Slice at y=$y xz")
subplot(2,2,2)
imshow(cyz', interpolation="nearest")
title("Slice at x=$x yz")
subplot(2,2,4)
imshow(cxy, interpolation="nearest")
title("Slice at z=$z xy")

subplots_adjust(wspace=0.18,hspace=0.3,left=0.06,bottom=0.06,right=1.0,top=0.93)
fig = Figure()
g = GridLayout(fig[1,1])
ax = CairoMakie.Axis(g[1,1], title = "Slice at y=$y xz", width = 150, height = 150)
heatmap!(ax, cxz)
ax = CairoMakie.Axis(g[1, 2], title = "Slice at x=$x yz", width = 150, height = 150)
heatmap!(ax, cyz)
ax = CairoMakie.Axis(g[2,2], title = "Slice at z=$z xy", width = 150, height = 150)
heatmap!(ax, cxy)

resize_to_layout!(fig)
if filename != nothing
savefig(filename)
save(filename, fig)
end
end