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fix tests
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Dennis Eichhorn committed Apr 24, 2024
1 parent 4dff3d3 commit efd5580
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241 changes: 3 additions & 238 deletions Algorithm/Clustering/AffinityPropagation.php
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Expand Up @@ -22,244 +22,9 @@
* @link https://jingga.app
* @see ./clustering_overview.png
* @since 1.0.0
*
* @todo Implement
*/
final class AffinityPropagation implements ClusteringInterface
final class AffinityPropagation
{
/**
* Points of the cluster centers
*
* @var Point[]
* @since 1.0.0
*/
private array $clusterCenters = [];

/**
* Cluster points
*
* Points in clusters (helper to avoid looping the cluster array)
*
* @var array
* @since 1.0.0
*/
private array $clusters = [];

private array $similarityMatrix = [];

private array $responsibilityMatrix = [];

private array $availabilityMatrix = [];

/**
* Original points used for clusters
*
* @var Point[]
* @since 1.0.0
*/
private array $points = [];

/**
* Create similarity matrix from points
*
* @param Point[] $points Points to create the similarity matrix for
*
* @return array<int, array<int, int|float>>
*
* @since 1.0.0
*/
private function createSimilarityMatrix(array $points) : array
{
$n = \count($points);
$coordinates = \count($points[0]->coordinates);
$similarityMatrix = \array_fill(0, $n, []);

$temp = [];
for ($i = 0; $i < $n - 1; ++$i) {
for ($j = $i + 1; $j < $n; ++$j) {
$sum = 0.0;
for ($c = 0; $c < $coordinates; ++$c) {
$sum += ($points[$i]->getCoordinate($c) - $points[$j]->getCoordinate($c)) * ($points[$i]->getCoordinate($c) - $points[$j]->getCoordinate($c));
}

$similarityMatrix[$i][$j] = -$sum;
$similarityMatrix[$j][$i] = -$sum;
$temp[] = $similarityMatrix[$i][$j];
}
}

\sort($temp);

$size = $n * ($n - 1) / 2;
$median = $size % 2 === 0
? ($temp[(int) ($size / 2)] + $temp[(int) ($size / 2 - 1)]) / 2
: $temp[(int) ($size / 2)];

for ($i = 0; $i < $n; ++$i) {
$similarityMatrix[$i][$i] = $median;
}

return $similarityMatrix;
}

/**
* Generate clusters for points
*
* @param Point[] $points Points to cluster
* @param int $iterations Iterations for cluster generation
*
* @return void
*
* @since 1.0.0
*/
public function generateClusters(array $points, int $iterations = 100) : void
{
$this->points = $points;
$n = \count($points);

$this->similarityMatrix = $this->createSimilarityMatrix($points);
$this->responsibilityMatrix = $this->similarityMatrix;
$this->availabilityMatrix = $this->similarityMatrix;

for ($c = 0; $c < $iterations; ++$c) {
for ($i = 0; $i < $n; ++$i) {
for ($k = 0; $k < $n; ++$k) {
$max = \PHP_INT_MIN;
for ($j = 0; $j < $k; ++$j) {
if (($temp = $this->similarityMatrix[$i][$j] + $this->availabilityMatrix[$i][$j]) > $max) {
$max = $temp;
}
}

for ($j = $k + 1; $j < $n; ++$j) {
if (($temp = $this->similarityMatrix[$i][$j] + $this->availabilityMatrix[$i][$j]) > $max) {
$max = $temp;
}
}

$this->responsibilityMatrix[$i][$k] = (1 - 0.9) * ($this->similarityMatrix[$i][$k] - $max) + 0.9 * $this->responsibilityMatrix[$i][$k];
}
}

for ($i = 0; $i < $n; ++$i) {
for ($k = 0; $k < $n; ++$k) {
$sum = 0.0;

if ($i === $k) {
for ($j = 0; $j < $i; ++$j) {
$sum += \max(0.0, $this->responsibilityMatrix[$j][$k]);
}

for (++$j; $j < $n; ++$j) {
$sum += \max(0.0, $this->responsibilityMatrix[$j][$k]);
}

$this->availabilityMatrix[$i][$k] = (1 - 0.9) * $sum + 0.9 * $this->availabilityMatrix[$i][$k];
} else {
$max = \max($i, $k);
$min = \min($i, $k);

for ($j = 0; $j < $min; ++$j) {
$sum += \max(0.0, $this->responsibilityMatrix[$j][$k]);
}

for ($j = $min + 1; $j < $max; ++$j) {
$sum += \max(0.0, $this->responsibilityMatrix[$j][$k]);
}

for ($j = $max + 1; $j < $n; ++$j) {
$sum += \max(0.0, $this->responsibilityMatrix[$j][$k]);
}

$this->availabilityMatrix[$i][$k] = (1 - 0.9) * \min(0.0, $this->responsibilityMatrix[$k][$k] + $sum) + 0.9 * $this->availabilityMatrix[$i][$k];
}
}
}
}

// find center points (exemplar)
for ($i = 0; $i < $n; ++$i) {
$temp = $this->responsibilityMatrix[$i][$i] + $this->availabilityMatrix[$i][$i];

if ($temp > 0) {
$this->clusterCenters[$i] = $this->points[$i];
}
}
}

/**
* Find the nearest group for a point
*
* @param array<int, array<int, int|float>> $similarityMatrix Similarity matrix
* @param int $point Point id in the similarity matrix to compare
*
* @return int
*
* @since 1.0.0
*/
private function findNearestGroup(array $similarityMatrix, int $point) : int
{
$maxSim = \PHP_INT_MIN;
$group = 0;

foreach ($this->clusterCenters as $c => $_) {
if ($similarityMatrix[$point][$c] > $maxSim) {
$maxSim = $similarityMatrix[$point][$c];
$group = $c;
}
}

return $group;
}

/**
* {@inheritdoc}
*/
public function cluster(Point $point) : ?Point
{
$points = $this->points;
$points[] = $point;

$similarityMatrix = $this->createSimilarityMatrix($points);

$c = $this->findNearestGroup(
$similarityMatrix,
\count($points) - 1,
);

return $this->clusterCenters[$c];
}

/**
* {@inheritdoc}
*/
public function getClusters() : array
{
if (!empty($this->clusters)) {
return $this->clusters;
}

$n = \count($this->points);
for ($i = 0; $i < $n; ++$i) {
$group = $this->findNearestGroup($this->points, $i);

$this->clusters[$group] = $this->points[$i];
}

return $this->clusters;
}

/**
* {@inheritdoc}
*/
public function getCentroids() : array
{
return $this->clusterCenters;
}

/**
* {@inheritdoc}
*/
public function getNoise() : array
{
return [];
}
}
2 changes: 1 addition & 1 deletion Router/WebRouter.php
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Original file line number Diff line number Diff line change
Expand Up @@ -141,7 +141,7 @@ public function route(
}

foreach ($destination as $d) {
if (!$d['active']) {
if (!($d['active'] ?? true)) {
continue;
}

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4 changes: 2 additions & 2 deletions tests/Router/WebRouterTest.php
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Original file line number Diff line number Diff line change
Expand Up @@ -156,7 +156,7 @@ public function testWithCSRF() : void
[['dest' => '\Modules\Admin\Controller:viewCsrf']],
$this->router->route(
(new HttpRequest(
new HttpUri('http://test.com/backend/admin/settings/csrf/something?test')
new HttpUri('http://test.com/backend/admin/settings/csrf?test')
))->uri->getRoute(),
'csrf_string'
)
Expand All @@ -173,7 +173,7 @@ public function testWithoutCSRF() : void
['dest' => RouteStatus::INVALID_CSRF],
$this->router->route(
(new HttpRequest(
new HttpUri('http://test.com/backend/admin/settings/csrf/something?test')
new HttpUri('http://test.com/backend/admin/settings/csrf?test')
))->uri->getRoute()
)
);
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14 changes: 14 additions & 0 deletions tests/Utils/Parser/Document/DocumentWriterTest.php
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Expand Up @@ -24,6 +24,20 @@
*/
final class DocumentWriterTest extends \PHPUnit\Framework\TestCase
{
protected function setUp() : void
{
if (\is_file(__DIR__ . '/data/WordMpdf.pdf')) {
\unlink(__DIR__ . '/data/WordMpdf.pdf');
}
}

protected function tearDown() : void
{
if (\is_file(__DIR__ . '/data/WordMpdf.pdf')) {
\unlink(__DIR__ . '/data/WordMpdf.pdf');
}
}

public function testParsing() : void
{
$doc = IOFactory::load(__DIR__ . '/data/Word.docx');
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14 changes: 14 additions & 0 deletions tests/Utils/Parser/Spreadsheet/SpreadsheetWriterTest.php
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,20 @@
*/
final class SpreadsheetWriterTest extends \PHPUnit\Framework\TestCase
{
protected function setUp() : void
{
if (\is_file(__DIR__ . '/data/ExcelMpdf.pdf')) {
\unlink(__DIR__ . '/data/ExcelMpdf.pdf');
}
}

protected function tearDown() : void
{
if (\is_file(__DIR__ . '/data/ExcelMpdf.pdf')) {
\unlink(__DIR__ . '/data/ExcelMpdf.pdf');
}
}

public function testParsing() : void
{
$sheet = IOFactory::load(__DIR__ . '/data/Excel.xlsx');
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