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/* Copyright (c) 2008-2025 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "as is"
* basis, without warranty of any kind, either expressed, implied, or
* statutory, including, without limitation, warranties that the
* Covered Software is free of defects, merchantable, fit for a
* particular purpose or non-infringing.
* See the Mozilla Public License v. 2.0 for more details.
*
* For more details, see http://www.mrtrix.org/.
*/
#include <set>
#include "command.h"
#include "exception.h"
#include "types.h"
#include "math/factorial.h"
#include "math/math.h"
#include "math/stats/shuffle.h"
#include "math/stats/typedefs.h"
using namespace MR;
using namespace App;
using namespace Math::Stats;
using MR::Math::Stats::matrix_type;
using MR::Math::Stats::index_array_type;
#define ROWS size_t(6)
#define BLOCK_INDICES 0,1,0,1,2,2 // Must increment from zero, and must be equal number in each
enum exchange_t { NONE, WITHIN, WHOLE };
vector<std::string> exchange_strings { "Unrestricted", "within-block", "whole-block" };
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
SYNOPSIS = "Verify correct operation of shuffling mechanisms for permutation testing";
REQUIRES_AT_LEAST_ONE_ARGUMENT = false;
}
void run ()
{
vector<std::string> failed_tests;
vector_type dummy_data (ROWS);
for (ssize_t row = 0; row != ROWS; ++row)
dummy_data[row] = default_type(row+1);
index_array_type block_indices (ROWS);
block_indices << BLOCK_INDICES;
assert (block_indices.size() == ROWS);
vector<std::set<size_t>> blocks (block_indices.maxCoeff()+1);
for (ssize_t i = 0; i != block_indices.size(); ++i)
blocks[block_indices[i]].insert (i);
auto test = [&] (const bool result, const std::string msg)
{
if (!result)
failed_tests.push_back (msg);
};
auto test_permutation_within = [&] (Shuffler& in, const std::string& msg)
{
in.reset();
Shuffle shuffle;
Eigen::Array<int, Eigen::Dynamic, 1> shuffled_data;
while (in (shuffle)) {
shuffled_data = (shuffle.data * dummy_data.matrix()).cast<int>();
for (size_t i = 0; i != ROWS; ++i) {
if (block_indices[std::abs(shuffled_data[i])-1] != block_indices[i]) {
failed_tests.push_back (msg);
return;
}
}
}
};
auto test_signflip_whole = [&] (Shuffler& in, const std::string& msg)
{
in.reset();
Shuffle shuffle;
Eigen::Array<int, Eigen::Dynamic, 1> shuffled_data;
while (in (shuffle)) {
shuffled_data = (shuffle.data * dummy_data.matrix()).cast<int>();
for (const auto& b : blocks) {
// Ensure that either all values in the block have been flipped,
// or none have been flipped
auto it = b.begin();
const bool flipped = shuffled_data[*it] < 0.0;
for (++it; it != b.end(); ++it) {
if (bool (shuffled_data[*it] < 0.0) != flipped) {
failed_tests.push_back (msg);
return;
}
}
}
}
};
auto test_permutation_whole = [&] (Shuffler& in, const std::string& msg)
{
in.reset();
Shuffle shuffle;
Eigen::Array<int, Eigen::Dynamic, 1> shuffled_data;
while (in (shuffle)) {
shuffled_data = (shuffle.data * dummy_data.matrix()).cast<int>();
for (const auto& b1 : blocks) {
// Only test each block once; use the first index within the block
const size_t first_in = *b1.begin();
// What got mapped into this location by the shuffling?
const size_t first_out = std::abs (shuffled_data[first_in]) - 1;
// Find the block from which this value originated
for (const auto& b2 : blocks) {
if (b2.find (first_out) != b2.end()) {
// Index at the start of block b1 in the shuffled data originated from block b2 before shuffling
// Ensure that ALL indices in block b1 in the shuffled data originated from block b2
for (auto i : b1) {
if (b2.find (std::abs (shuffled_data[i])-1) == b2.end()) {
failed_tests.push_back (msg);
return;
}
}
break;
}
}
}
}
};
auto test_unique = [&] (Shuffler& in, const std::string& msg)
{
in.reset();
vector<Shuffle> matrices;
Shuffle temp;
bool duplicate_index = false, duplicate_data = false;
while (in (temp)) {
for (const auto& previous : matrices) {
if (temp.index == previous.index)
duplicate_index = true;
if (temp.data == previous.data)
duplicate_data = true;
matrices.push_back (temp);
}
}
if (duplicate_index)
failed_tests.push_back (msg + " (duplicate shuffle index)");
if (duplicate_data)
failed_tests.push_back (msg + " (duplicate shuffle matrix data)");
};
auto test_kernel = [&] (const size_t requested_number,
const size_t expected_number,
const Shuffler::error_t error_type,
const index_array_type& eb_within,
const index_array_type& eb_whole,
const std::string& error_string,
const std::string& eb_string,
const std::string& test_string,
const bool test_uniqueness)
{
LogLevelLatch latch (requested_number > expected_number ? 0 : App::log_level);
Shuffler temp (ROWS, requested_number, error_type, false, eb_within, eb_whole);
test (temp.size() == expected_number, "Incorrect number of shuffles; " + error_string + "; " + eb_string + "; " + test_string);
if (eb_within.size())
test_permutation_within (temp, "Broken within-block permutation; " + error_string + "; " + test_string);
if (eb_whole.size()) {
if (error_type == Shuffler::error_t::EE || error_type == Shuffler::error_t::BOTH)
test_permutation_whole (temp, "Broken whole-block exchangeability; " + error_string + "; " + test_string);
if (error_type == Shuffler::error_t::ISE || error_type == Shuffler::error_t::BOTH)
test_signflip_whole (temp, "Broken whole-block sign-flipping; " + error_string + "; " + test_string);
}
if (test_uniqueness)
test_unique (temp, "Bad shuffles; " + error_string + "; " + eb_string + "; " + test_string);
};
for (size_t exchange_index = 0; exchange_index != 3; ++exchange_index) {
const index_array_type eb_within (exchange_t(exchange_index) == exchange_t::WITHIN ?
block_indices :
index_array_type());
const index_array_type eb_whole (exchange_t(exchange_index) == exchange_t::WHOLE ?
block_indices :
index_array_type());
const std::string eb_string (exchange_strings[exchange_index]);
size_t max_num_permutations, max_num_signflips;
switch (exchange_index) {
case exchange_t::NONE:
max_num_permutations = Math::factorial (ROWS);
max_num_signflips = size_t(1) << ROWS;
break;
case exchange_t::WITHIN:
max_num_permutations = 1;
for (const auto& b : blocks)
max_num_permutations *= Math::factorial (b.size());
max_num_signflips = size_t(1) << ROWS;
break;
case exchange_t::WHOLE:
max_num_permutations = Math::factorial (blocks.size());
max_num_signflips = size_t(1) << blocks.size();
break;
}
const size_t max_num_combined = max_num_permutations * max_num_signflips;
// EE and ISE
for (size_t error_index = 0; error_index != 2; ++error_index) {
const Shuffler::error_t error_type (error_index ? Shuffler::error_t::ISE : Shuffler::error_t::EE);
const std::string error_string (error_index ? "ISE" : "EE");
const size_t max_num (error_index ? max_num_signflips : max_num_permutations);
test_kernel (max_num/2, max_num/2, error_type, eb_within, eb_whole, error_string, eb_string, "less than max shuffles", true);
test_kernel (max_num, max_num, error_type, eb_within, eb_whole, error_string, eb_string, "exactly max shuffles", true);
test_kernel (2*max_num, max_num, error_type, eb_within, eb_whole, error_string, eb_string, "more than max shuffles", true);
}
// BOTH
{
test_kernel (max_num_signflips/2, max_num_signflips/2, Shuffler::error_t::BOTH, eb_within, eb_whole, "BOTH", eb_string, "less than max signflips", true);
test_kernel (max_num_signflips, max_num_signflips, Shuffler::error_t::BOTH, eb_within, eb_whole, "BOTH", eb_string, "exactly max signflips", true);
test_kernel ((max_num_signflips + max_num_permutations)/2, (max_num_signflips + max_num_permutations)/2, Shuffler::error_t::BOTH, eb_within, eb_whole, "BOTH", eb_string, "between max signflips and max permutations", true);
test_kernel (max_num_permutations, max_num_permutations, Shuffler::error_t::BOTH, eb_within, eb_whole, "BOTH", eb_string, "exactly max permutations", true);
// Note: Only test where uniqueness of shuffles is not guaranteed
// (both signflips and permutations will individually have random duplicates)
test_kernel ((max_num_permutations + max_num_combined)/2, (max_num_permutations + max_num_combined)/2, Shuffler::error_t::BOTH, eb_within, eb_whole, "BOTH", eb_string, "between max permutations and max shuffles", false);
test_kernel (max_num_combined, max_num_combined, Shuffler::error_t::BOTH, eb_within, eb_whole, "BOTH", eb_string, "exactly max shuffles", true);
test_kernel (2 * max_num_combined, max_num_combined, Shuffler::error_t::BOTH, eb_within, eb_whole, "BOTH", eb_string, "more than max shuffles", true);
}
}
if (failed_tests.size()) {
Exception e (str(failed_tests.size()) + " tests of shuffling mechanisms failed:");
for (auto s : failed_tests)
e.push_back (s);
throw e;
}
}
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