From 18fd4f141736a9d56a86789ef079a1f472a67e50 Mon Sep 17 00:00:00 2001
From: Nicola Vigano <nicola.vigano@esrf.fr>
Date: Tue, 12 Feb 2013 16:59:15 +0100
Subject: [PATCH] Astra: updated benchmarks against new cell interface
Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>
---
zUtil_DataStructures/GtAstraBenchmarks.m | 314 +++++++++++++++++++++--
zUtil_DataStructures/GtBenchmarks.m | 3 +-
2 files changed, 288 insertions(+), 29 deletions(-)
diff --git a/zUtil_DataStructures/GtAstraBenchmarks.m b/zUtil_DataStructures/GtAstraBenchmarks.m
index 76cadf9c..6a40f50c 100644
--- a/zUtil_DataStructures/GtAstraBenchmarks.m
+++ b/zUtil_DataStructures/GtAstraBenchmarks.m
@@ -1,21 +1,11 @@
classdef GtAstraBenchmarks < GtBenchmarks
methods (Access = public, Static)
- function benchmark3Dset(numIters, sirtDetectImages)
- if (~exist('numIters', 'var'))
- numIters = 20;
- end
- if (~exist('sirtDetectImages', 'var'))
- sirtDetectImages = rand(1e2, 2e2, 3e2);
- end
- proj = [];
- proj.stack = sirtDetectImages;
- proj.num_cols = size(sirtDetectImages, 1);
- proj.num_rows = size(sirtDetectImages, 3);
- proj.geom = ones(size(sirtDetectImages, 2), 12);
- proj_geom = astra_create_proj_geom('parallel3d_vec', proj.num_rows, proj.num_cols, proj.geom);
+ %%% SINO
+ function benchmark3Dcreate(numIters, sirtDetectImages)
+ [proj, proj_geom] = GtAstraBenchmarks.createProjAndGeom(sirtDetectImages);
bytes = GtBenchmarks.getSizeVariable(sirtDetectImages);
- GtBenchmarks.printHeader('Set Mex Data 3D', bytes)
+ GtBenchmarks.printHeader('Create Mex Data 3D', bytes)
fprintf(' - Doing %d iterations: ', numIters)
tic();
@@ -26,7 +16,28 @@ classdef GtAstraBenchmarks < GtBenchmarks
GtBenchmarks.printResult('astra_mex_data3d(''create'', ''-proj3d'')', toc()/numIters, bytes);
% Let's assume 'get' is correct!
- proj_id = astra_mex_data3d('create', '-proj3d', proj_geom, proj.stack);
+ proj_id = astra_mex_data3d('create', '-proj3d', proj_geom, proj.stack);
+ copied = astra_mex_data3d('get', proj_id);
+ astra_mex_data3d('delete', proj_id);
+
+ GtBenchmarks.verifyError(sirtDetectImages, copied);
+ end
+
+ function benchmark3Dstore(numIters, sirtDetectImages)
+ [proj, proj_geom] = GtAstraBenchmarks.createProjAndGeom(sirtDetectImages);
+
+ bytes = GtBenchmarks.getSizeVariable(sirtDetectImages);
+ GtBenchmarks.printHeader('Store Mex Data 3D', bytes)
+ fprintf(' - Doing %d iterations: ', numIters)
+
+ proj_id = astra_mex_data3d('create', '-proj3d', proj_geom, proj.stack);
+ tic();
+ for ii = 1:numIters
+ astra_mex_data3d('store', proj_id, proj.stack);
+ end
+ GtBenchmarks.printResult('astra_mex_data3d(''store'', ''-proj3d'')', toc()/numIters, bytes);
+
+ % Let's assume 'get' is correct!
copied = astra_mex_data3d('get', proj_id);
astra_mex_data3d('delete', proj_id);
@@ -34,23 +45,72 @@ classdef GtAstraBenchmarks < GtBenchmarks
end
function benchmark3Dget(numIters, sirtDetectImages)
- if (~exist('numIters', 'var'))
- numIters = 20;
+ [proj, proj_geom] = GtAstraBenchmarks.createProjAndGeom(sirtDetectImages);
+
+ bytes = GtBenchmarks.getSizeVariable(sirtDetectImages);
+ GtBenchmarks.printHeader('Get Mex Data 3D', bytes)
+ fprintf(' - Doing %d iterations: ', numIters)
+ proj_id = astra_mex_data3d('create', '-proj3d', proj_geom, proj.stack);
+
+ tic();
+ for ii = 1:numIters
+ proj = astra_mex_data3d('get', proj_id);
end
- if (~exist('sirtDetectImages', 'var'))
- sirtDetectImages = rand(1e2, 2e2, 3e2);
+ astra_mex_data3d('delete', proj_id);
+ GtBenchmarks.printResult('astra_mex_data3d(''get'', proj_id)', toc()/numIters, bytes);
+ end
+
+ %%% VOL
+ function benchmarkVolCreate(numIters, sirtDetectImages)
+ vol_geom = GtAstraBenchmarks.createVolAndGeom(sirtDetectImages);
+
+ bytes = GtBenchmarks.getSizeVariable(sirtDetectImages);
+ GtBenchmarks.printHeader('Create Mex Data 3D', bytes)
+ fprintf(' - Doing %d iterations: ', numIters)
+
+ tic();
+ for ii = 1:numIters
+ proj_id = astra_mex_data3d('create', '-vol', vol_geom, sirtDetectImages);
+ astra_mex_data3d('delete', proj_id);
end
- proj = [];
- proj.stack = sirtDetectImages;
- proj.num_cols = size(sirtDetectImages, 1);
- proj.num_rows = size(sirtDetectImages, 3);
- proj.geom = ones(size(sirtDetectImages, 2), 12);
- proj_geom = astra_create_proj_geom('parallel3d_vec', proj.num_rows, proj.num_cols, proj.geom);
+ GtBenchmarks.printResult('astra_mex_data3d(''create'', ''-vol'')', toc()/numIters, bytes);
+
+ % Let's assume 'get' is correct!
+ proj_id = astra_mex_data3d('create', '-vol', vol_geom, sirtDetectImages);
+ copied = astra_mex_data3d('get', proj_id);
+ astra_mex_data3d('delete', proj_id);
+
+ GtBenchmarks.verifyError(sirtDetectImages, copied);
+ end
+
+ function benchmarkVolStore(numIters, sirtDetectImages)
+ vol_geom = GtAstraBenchmarks.createVolAndGeom(sirtDetectImages);
+
+ bytes = GtBenchmarks.getSizeVariable(sirtDetectImages);
+ GtBenchmarks.printHeader('Store Mex Data 3D', bytes)
+ fprintf(' - Doing %d iterations: ', numIters)
+
+ proj_id = astra_mex_data3d('create', '-vol', vol_geom);
+ tic();
+ for ii = 1:numIters
+ astra_mex_data3d('store', proj_id, sirtDetectImages);
+ end
+ GtBenchmarks.printResult('astra_mex_data3d(''store'', ''-vol'')', toc()/numIters, bytes);
+
+ % Let's assume 'get' is correct!
+ copied = astra_mex_data3d('get', proj_id);
+ astra_mex_data3d('delete', proj_id);
+
+ GtBenchmarks.verifyError(sirtDetectImages, copied);
+ end
+
+ function benchmarkVolGet(numIters, sirtDetectImages)
+ vol_geom = GtAstraBenchmarks.createVolAndGeom(sirtDetectImages);
bytes = GtBenchmarks.getSizeVariable(sirtDetectImages);
GtBenchmarks.printHeader('Get Mex Data 3D', bytes)
fprintf(' - Doing %d iterations: ', numIters)
- proj_id = astra_mex_data3d('create', '-proj3d', proj_geom, proj.stack);
+ proj_id = astra_mex_data3d('create', '-vol', vol_geom, sirtDetectImages);
tic();
for ii = 1:numIters
@@ -60,11 +120,209 @@ classdef GtAstraBenchmarks < GtBenchmarks
GtBenchmarks.printResult('astra_mex_data3d(''get'', proj_id)', toc()/numIters, bytes);
end
+ %%% CELL SINO
+ function benchmarkCellCreate(numIters, detectImages, numCells)
+ proj = cell(1, numCells);
+ proj_geom = cell(1, numCells);
+ for n = 1:numCells
+ [proj{n}, proj_geom{n}] = GtAstraBenchmarks.createProjAndGeom(detectImages);
+ end
+ proj_stack = cell(1, numCells);
+ for n = 1:numCells
+ proj_stack{n} = proj{n}.stack;
+ end
+
+ bytes = numCells * GtBenchmarks.getSizeVariable(detectImages);
+ GtBenchmarks.printHeader('Create Mex Data Cell', bytes)
+ fprintf(' - Doing %d iterations: ', numIters)
+
+ tic();
+ for ii = 1:numIters
+ proj_id = astra_mex_data3d('create', '-proj3d', proj_geom, proj_stack);
+ astra_mex_data3d('delete', proj_id{:});
+ end
+ GtBenchmarks.printResult('astra_mex_data3d(''create'', ''-proj3d'')', toc()/numIters, bytes);
+
+ % Let's assume 'get' is correct!
+ proj_id = astra_mex_data3d('create', '-proj3d', proj_geom, proj_stack);
+ copied = astra_mex_data3d('get', proj_id);
+ astra_mex_data3d('delete', proj_id{:});
+
+ GtBenchmarks.verifyError(proj_stack, copied);
+ end
+
+ function benchmarkCellStore(numIters, detectImages, numCells)
+ proj = cell(1, numCells);
+ proj_geom = cell(1, numCells);
+ for n = 1:numCells
+ [proj{n}, proj_geom{n}] = GtAstraBenchmarks.createProjAndGeom(detectImages);
+ end
+ proj_stack = cell(1, numCells);
+ for n = 1:numCells
+ proj_stack{n} = proj{n}.stack;
+ end
+
+ bytes = numCells * GtBenchmarks.getSizeVariable(detectImages);
+ GtBenchmarks.printHeader('Store Mex Data Cell', bytes)
+ fprintf(' - Doing %d iterations: ', numIters)
+
+ proj_id = astra_mex_data3d('create', '-proj3d', proj_geom, proj_stack);
+ tic();
+ for ii = 1:numIters
+ astra_mex_data3d('store', proj_id, proj_stack);
+ end
+ GtBenchmarks.printResult('astra_mex_data3d(''store'', ''-proj3d'')', toc()/numIters, bytes);
+
+ % Let's assume 'get' is correct!
+ copied = astra_mex_data3d('get', proj_id);
+ astra_mex_data3d('delete', proj_id{:});
+
+ GtBenchmarks.verifyError(proj_stack, copied);
+ end
+
+ function benchmarkCellGet(numIters, detectImages, numCells)
+ proj = cell(1, numCells);
+ proj_geom = cell(1, numCells);
+ for n = 1:numCells
+ [proj{n}, proj_geom{n}] = GtAstraBenchmarks.createProjAndGeom(detectImages);
+ end
+ proj_stack = cell(1, numCells);
+ for n = 1:numCells
+ proj_stack{n} = proj{n}.stack;
+ end
+
+ bytes = numCells * GtBenchmarks.getSizeVariable(detectImages);
+ GtBenchmarks.printHeader('Get Mex Data Cell', bytes)
+ fprintf(' - Doing %d iterations: ', numIters)
+ proj_id = astra_mex_data3d('create', '-proj3d', proj_geom, proj_stack);
+
+ tic();
+ for ii = 1:numIters
+ proj = astra_mex_data3d('get', proj_id);
+ end
+ GtBenchmarks.printResult('astra_mex_data3d(''get'', proj_id)', toc()/numIters, bytes);
+ astra_mex_data3d('delete', proj_id{:});
+ end
+
+ %%% CELL VOL
+ function benchmarkCellVolCreate(numIters, detectImages, numCells)
+ vol_geom = cell(1, numCells);
+ for n = 1:numCells
+ vol_geom{n} = GtAstraBenchmarks.createVolAndGeom(detectImages);
+ end
+ vol_stack = cell(1, numCells);
+ for n = 1:numCells
+ vol_stack{n} = detectImages;
+ end
+
+ bytes = numCells * GtBenchmarks.getSizeVariable(detectImages);
+ GtBenchmarks.printHeader('Create Mex Data Cell', bytes)
+ fprintf(' - Doing %d iterations: ', numIters)
+
+ tic();
+ for ii = 1:numIters
+ proj_id = astra_mex_data3d('create', '-vol', vol_geom, vol_stack);
+ astra_mex_data3d('delete', proj_id{:});
+ end
+ GtBenchmarks.printResult('astra_mex_data3d(''create'', ''-vol'')', toc()/numIters, bytes);
+
+ % Let's assume 'get' is correct!
+ proj_id = astra_mex_data3d('create', '-vol', vol_geom, vol_stack);
+ copied = astra_mex_data3d('get', proj_id);
+ astra_mex_data3d('delete', proj_id{:});
+
+ GtBenchmarks.verifyError(vol_stack, copied);
+ end
+
+ function benchmarkCellVolStore(numIters, detectImages, numCells)
+ vol_geom = cell(1, numCells);
+ for n = 1:numCells
+ vol_geom{n} = GtAstraBenchmarks.createVolAndGeom(detectImages);
+ end
+ vol_stack = cell(1, numCells);
+ for n = 1:numCells
+ vol_stack{n} = detectImages;
+ end
+
+ bytes = numCells * GtBenchmarks.getSizeVariable(detectImages);
+ GtBenchmarks.printHeader('Store Mex Data Cell', bytes)
+ fprintf(' - Doing %d iterations: ', numIters)
+
+ proj_id = astra_mex_data3d('create', '-vol', vol_geom);
+ tic();
+ for ii = 1:numIters
+ astra_mex_data3d('store', proj_id, vol_stack);
+ end
+ GtBenchmarks.printResult('astra_mex_data3d(''store'', ''-vol'')', toc()/numIters, bytes);
+
+ % Let's assume 'get' is correct!
+ copied = astra_mex_data3d('get', proj_id);
+ astra_mex_data3d('delete', proj_id{:});
+
+ GtBenchmarks.verifyError(vol_stack, copied);
+ end
+
+ function benchmarkCellVolGet(numIters, detectImages, numCells)
+ vol_geom = cell(1, numCells);
+ for n = 1:numCells
+ vol_geom{n} = GtAstraBenchmarks.createVolAndGeom(detectImages);
+ end
+ vol_stack = cell(1, numCells);
+ for n = 1:numCells
+ vol_stack{n} = detectImages;
+ end
+
+ bytes = numCells * GtBenchmarks.getSizeVariable(detectImages);
+ GtBenchmarks.printHeader('Get Mex Data Cell', bytes)
+ fprintf(' - Doing %d iterations: ', numIters)
+ proj_id = astra_mex_data3d('create', '-vol', vol_geom, vol_stack);
+
+ tic();
+ for ii = 1:numIters
+ proj = astra_mex_data3d('get', proj_id);
+ end
+ GtBenchmarks.printResult('astra_mex_data3d(''get'', proj_id)', toc()/numIters, bytes);
+ astra_mex_data3d('delete', proj_id{:});
+ end
+
function allBenchmarks()
- imgs = rand(5e2, 5e2, 5e2);
+ imgs = rand(1e3, 1e3, 1e2);
- GtAstraBenchmarks.benchmark3Dset(5, imgs)
+ GtAstraBenchmarks.benchmark3Dcreate(5, imgs)
+ GtAstraBenchmarks.benchmark3Dstore(5, imgs)
GtAstraBenchmarks.benchmark3Dget(5, imgs)
+
+ GtAstraBenchmarks.benchmarkVolCreate(5, imgs)
+ GtAstraBenchmarks.benchmarkVolStore(5, imgs)
+ GtAstraBenchmarks.benchmarkVolGet(5, imgs)
+
+ imgs = rand(1e3, 1e3, 2e1);
+
+ GtAstraBenchmarks.benchmarkCellCreate(5, imgs, 5);
+ GtAstraBenchmarks.benchmarkCellStore(5, imgs, 5);
+ GtAstraBenchmarks.benchmarkCellGet(5, imgs, 5);
+
+ GtAstraBenchmarks.benchmarkCellVolCreate(5, imgs, 5);
+ GtAstraBenchmarks.benchmarkCellVolStore(5, imgs, 5);
+ GtAstraBenchmarks.benchmarkCellVolGet(5, imgs, 5);
+
+ % Just in case
+ astra_mex_data3d('clear');
+ end
+ end
+
+ methods (Access = protected, Static)
+ function [proj, proj_geom] = createProjAndGeom(detectImages)
+ proj = [];
+ proj.stack = detectImages;
+ proj.num_cols = size(detectImages, 1);
+ proj.num_rows = size(detectImages, 3);
+ proj.geom = ones(size(detectImages, 2), 12);
+ proj_geom = astra_create_proj_geom('parallel3d_vec', proj.num_rows, proj.num_cols, proj.geom);
+ end
+
+ function vol_geom = createVolAndGeom(detectImages)
+ vol_geom = astra_create_vol_geom(size(detectImages, 1), size(detectImages, 2), size(detectImages, 3));
end
end
end
diff --git a/zUtil_DataStructures/GtBenchmarks.m b/zUtil_DataStructures/GtBenchmarks.m
index b1966bdc..4715b1f2 100644
--- a/zUtil_DataStructures/GtBenchmarks.m
+++ b/zUtil_DataStructures/GtBenchmarks.m
@@ -19,7 +19,8 @@ classdef GtBenchmarks
function verifyError(reference, computed)
fprintf('Checking errors in computation:\n')
if (iscell(reference))
- fprintf('\t%g\n', max(cellfun(@(x, y)max(max(max(abs(x - y)))), reference, computed)));
+ fprintf('\t%g\n', max(cellfun(@(x, y)max(max(max(abs(x - y)))), ...
+ reshape(reference, [numel(reference), 1]), reshape(computed, [numel(computed), 1]) )) );
elseif (isscalar(reference))
fprintf('\t%g (%g relative)\n', abs(reference - computed), abs((reference - computed)/reference) );
else
--
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