better benchmarking

MagneticResonanceImaging · Aug 16, 2020 · b24b60c · b24b60c
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commit b24b60c
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Showing 4 changed files with 15 additions and 7 deletions.
diff --git a/benchmark1/latex/reco_images.tex b/benchmark1/latex/reco_images.tex
@@ -68,6 +68,8 @@
 \node[rotate=90, left = 2mm of conc1, xshift=8mm]{MRIReco};
 
 
+
+
 \node[inner sep=1pt, below = 2pt of conc1] (conc1) 
 {\includegraphics[width=0.2\textwidth]{../reco/imgCG_diff_mrireco_rf1.png}};
 \node[right = 1pt of conc1, nodewhite] (conc2) 

diff --git a/benchmark1/recoBrainBart.m b/benchmark1/recoBrainBart.m
@@ -29,12 +29,18 @@
 rf = [1,2,3,4];
 times = zeros(1, length(rf));
 img_cg = {};
+numTrials = 20;
+
 for i=1:length(rf)
     traj_sub = trajectory(:,:,1:rf(i):nSpokes);
     rawdata_sub = rawdata(:,:,1:rf(i):nSpokes,:);
-    tic();
-    img_cg{i} = bart('pics -l2 -r 0.001 -i 20 -t', traj_sub, rawdata_sub, smaps);
-    times(i) = toc();
+    timesTrials = zeros(1, numTrials);
+    for k=1:numTrials
+      tic();
+      img_cg{i} = bart('pics -l2 -r 0.001 -i 20 -t', traj_sub, rawdata_sub, smaps);
+      timesTrials(k) = toc();
+    end
+    times(i) = min(timesTrials);
 end
 
 %% write output images and reco times to files

diff --git a/benchmark1/recoBrainMRIReco.jl b/benchmark1/recoBrainMRIReco.jl
@@ -1,5 +1,9 @@
 using HDF5, MRIReco, DelimitedFiles, BenchmarkTools
 
+# change BenchmarkTools settings to match what we do in the Matlab script
+BenchmarkTools.DEFAULT_PARAMETERS.seconds = 10000
+BenchmarkTools.DEFAULT_PARAMETERS.samples = 20
+
 filename = "./data/rawdata_brain_radial_96proj_12ch.h5"
 data = permutedims(h5read(filename, "rawdata"),[3,2,1,4])
 traj = permutedims(h5read(filename, "trajectory"),[3,2,1])

diff --git a/benchmark1/runBenchmark.sh b/benchmark1/runBenchmark.sh
@@ -12,10 +12,6 @@ do
   julia-1.5 --threads=${t} recoBrainMRIReco.jl &
   wait
   export TOEPLITZ=0
-  export OVERSAMPLING=2.0
-  julia-1.5 --threads=${t} recoBrainMRIReco.jl &
-  wait
-  export TOEPLITZ=0
   export OVERSAMPLING=1.25
   julia-1.5 --threads=${t} recoBrainMRIReco.jl &
   wait