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MeanFiller.cpp
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MeanFiller.cpp
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#include "MeanFiller.h"
#include "Utils.h"
MeanFiller::MeanFiller(): timer(), image(nullptr), res_image(nullptr), threshold(0), quantile(0), minx(0), miny(0), minz(0), maxx(0), maxy(0), maxz(0)
{
kernel = Utils::sobelKernel(1, 2);
history = deque<stack<triple>>();
candidates = set<triple>();
}
SegImage* MeanFiller::fill(int startX, int startY, int startZ, int startRadius)
{
timer.start("Fill");
int cols, rows, slices;
stack<triple> historyEntity;
cube sample;
image->getSize(cols, rows, slices);
cube result = zeros(rows, cols, slices);
cube sphere = Utils::sphere(startRadius);
result(startY, startX, startZ, arma::size(sphere)) = sphere;
timer.stage("Init");
res_image = Utils::convert(result);
timer.stage("Convert");
Utils::bounds(result, minx, miny, minz, maxx, maxy, maxz);
timer.stage("Bounds");
result.reset();
history.clear();
if (minx < 3) minx = 3;
if (maxx > cols - 2) maxx = cols - 2;
if (miny < 3) miny = 3;
if (maxy > rows - 2) maxy = rows - 2;
if (minz < 3) minz = 3;
if (maxz > slices - 2) maxz = slices - 2;
bool flag = false;
while(!flag)
{
historyEntity = stack<triple>();
flag = true;
for (int i = minx; i <= maxx; i++)
{
for (int j = miny; j <= maxy; j++)
{
for (int k = minz; k <= maxz; k++)
{
if (image->getVoxel(i,j,k) > 0 && res_image->getVoxel(i,j,k) == 0)
{
sample = wBright * Utils::convert_d(image->getRegion(i - 2, j - 2, i + 2, j + 2, k - 2, k + 2)) +
wCurv * Utils::convert_d(res_image->getRegion(i - 2, j - 2, i + 2, j + 2, k - 2, k + 2));
double der = derivate(sample);
if (der > threshold)
{
res_image->setVoxel(i, j, k, 255);
if (i <= minx && i >= 4 && minx > i - 1)
minx = i - 1;
if (i >= maxx && i <= cols - 4 && maxx < i + 1)
maxx = i + 1;
if (j <= miny && j >= 4 && miny > j - 1)
miny = j - 1;
if (j >= maxy && j <= rows - 4 && maxy < j + 1)
maxy = j + 1;
if (k <= minz && k >= 4 && minz > k - 1)
minz = k - 1;
if (k >= maxz && k <= slices - 4 && minz < k + 1)
maxz = k + 1;
historyEntity.push(triple(i, j, k));
flag = false;
}
}
}
}
}
timer.stage("Full cycle");
if (!flag) {
if (history.size() >= h_size)
{
stack<triple> first = history.back();
while (!first.empty())
{
first.pop();
}
history.pop_back();
}
history.push_front(historyEntity);
}
}
timer.stop();
return res_image;
}
SegImage* MeanFiller::fillDynamic(int startX, int startY, int startZ, int startRadius)
{
int cols, rows, slices;
int minx, miny, minz, maxx, maxy, maxz;
cube sample, xes;
vec values;
stack<triple> historyEntity;
image->getSize(cols, rows, slices);
cube result = zeros(rows, cols, slices);
cube sphere = Utils::sphere(startRadius);
result(startY, startX, startZ, arma::size(sphere)) = sphere;
res_image = Utils::convert(result);
Utils::bounds(result, minx, miny, minz, maxx, maxy, maxz);
double thres;
history.clear();
result.reset();
if (minx < 3) minx = 3;
if (maxx > cols - 2) maxx = cols - 2;
if (miny < 3) miny = 3;
if (maxy > rows - 2) maxy = rows - 2;
if (minz < 3) minz = 3;
if (maxz > slices - 2) maxz = slices - 2;
bool flag = false;
while (!flag)
{
flag = true;
xes = Utils::convert_d(image->getRegion(minx, miny, maxx, maxy, minz, maxz));
sample = wBright * Utils::convert_d(res_image->getRegion(minx, miny, maxx, maxy, minz, maxz)) +
wCurv * xes;
sample = Utils::conv3(Utils::conv3(sample, kernel), kernel);
sample %= -xes + 1;
values = sort(nonzeros(vectorise(sample)));
thres = values(quantile * values.size());
for (int i = minx; i < maxx; i++)
{
for (int j = miny; j < maxy; j++)
{
for (int k = minz; k < maxz; k++)
{
if (image->getVoxel(i, j, k) > 0 && res_image->getVoxel(i, j, k) == 0)
{
if (sample(j-miny, i - minx, k - minz) > thres)
{
res_image->setVoxel(i, j, k, 255);
if (i <= minx && i >= 4)
minx = i - 1;
if (i >= maxx && i <= cols - 4 && maxx < i + 1)
maxx = i + 1;
if (j <= miny && j >= 4)
miny = j - 1;
if (j >= maxy && j <= rows - 4 && maxy < j + 1)
maxy = j + 1;
if (k <= minz && k >= 4)
minz = k - 1;
if (k >= maxz && k <= slices - 4 && maxz < k + 1)
maxz = k + 1;
historyEntity.push(triple(i, j, k));
flag = false;
}
}
}
}
}
if (!flag) {
if (history.size() >= h_size)
{
stack<triple> first = history.back();
while (!first.empty())
{
first.pop();
}
history.pop_back();
}
history.push_front(historyEntity);
}
}
return res_image;
}
SegImage* MeanFiller::fillAlt(int startX, int startY, int startZ, int startRadius)
{
timer.start("Fill Alt");
int cols, rows, slices;
cube sample;
image->getSize(cols, rows, slices);
cube result = zeros(rows, cols, slices);
cube sphere = Utils::sphere(startRadius);
result(startY, startX, startZ, arma::size(sphere)) = sphere;
timer.stage("Init");
res_image = Utils::convert(result);
timer.stage("Convert");
Utils::bounds(result, minx, miny, minz, maxx, maxy, maxz);
timer.stage("Bounds");
result.reset();
history.clear();
if (minx < 3) minx = 3;
if (maxx > cols - 2) maxx = cols - 2;
if (miny < 3) miny = 3;
if (maxy > rows - 2) maxy = rows - 2;
if (minz < 3) minz = 3;
if (maxz > slices - 2) maxz = slices - 2;
for (int i = minx; i <= maxx; i++)
{
for (int j = miny; j <= maxy; j++)
{
for (int k = minz; k <= maxz; k++)
{
addNeighbors(i, j, k);
}
}
}
timer.stage("First candidates");
while (!candidates.empty()) {
set<triple>::iterator last = --candidates.end();
triple c = *last;
candidates.erase(last);
sample = wBright * Utils::convert_d(image->getRegion(c.x - 2, c.y - 2, c.x + 2, c.y + 2, c.z - 2, c.z + 2)) +
wCurv * Utils::convert_d(res_image->getRegion(c.x - 2, c.y - 2, c.x + 2, c.y + 2, c.z - 2, c.z + 2));
double der = derivate(sample);
if (der > threshold)
{
res_image->setVoxel(c.x, c.y, c.z, 255);
addNeighbors(c.x, c.y, c.z);
}
}
timer.stop();
return res_image;
}
SegImage* MeanFiller::get_image() const
{
return image;
}
void MeanFiller::set_image(SegImage* image)
{
this->image = image;
}
double MeanFiller::get_threshold() const
{
return threshold;
}
void MeanFiller::set_threshold(double threshold)
{
this->threshold = threshold;
}
double MeanFiller::get_quantile() const
{
return quantile;
}
void MeanFiller::set_quantile(double quantile)
{
this->quantile = quantile;
}
SegImage* MeanFiller::iterate_fw()
{
if (!iterate(threshold))
{
threshold *= 0.9;
iterate(threshold);
}
return res_image;
}
SegImage* MeanFiller::iterate_bw()
{
if (!history.empty()) {
stack<triple> last = history.front();
history.pop_front();
while (!last.empty())
{
triple coords = last.top();
last.pop();
res_image->setVoxel(coords.x, coords.y, coords.z, 0);
}
}
return res_image;
}
void MeanFiller::reset() const
{
delete image;
delete res_image;
}
double MeanFiller::derivate(cube input) const
{
if (input.n_rows != 5 || input.n_cols != 5 || input.n_slices != 5)
{
throw invalid_argument("The derivative is calculated over strictly 5x5x5 matrices");
}
return Utils::conv3(Utils::conv3(input, kernel).subcube(1, 1, 1, 3, 3, 3), kernel)(1, 1, 1);
}
bool MeanFiller::iterate(double thres)
{
stack<triple> historyEntity = stack<triple>();
cube sample;
int cols, rows, slices;
image->getSize(cols, rows, slices);
bool flag = false;
for (int i = minx; i <= maxx; i++)
{
for (int j = miny; j <= maxy; j++)
{
for (int k = minz; k <= maxz; k++)
{
if (image->getVoxel(i, j, k) > 0 && res_image->getVoxel(i, j, k) == 0)
{
sample = wBright * Utils::convert_d(image->getRegion(i - 2, j - 2, i + 2, j + 2, k - 2, k + 2)) +
wCurv * Utils::convert_d(res_image->getRegion(i - 2, j - 2, i + 2, j + 2, k - 2, k + 2));
double der = derivate(sample);
if (der > thres)
{
res_image->setVoxel(i, j, k, 255);
if (i <= minx && i >= 4 && minx > i - 1)
minx = i - 1;
if (i >= maxx && i <= cols - 4 && maxx < i + 1)
maxx = i + 1;
if (j <= miny && j >= 4 && miny > j - 1)
miny = j - 1;
if (j >= maxy && j <= rows - 4 && maxy < j + 1)
maxy = j + 1;
if (k <= minz && k >= 4 && minz > k - 1)
minz = k - 1;
if (k >= maxz && k <= slices - 4 && maxz < k + 1)
maxz = k + 1;
historyEntity.push(triple(i, j, k));
flag = true;
}
}
}
}
}
if (flag)
{
if (history.size() >= h_size)
{
history.pop_back();
}
history.push_front(historyEntity);
}
return flag;
}
void MeanFiller::addNeighbors(int x, int y, int z)
{
for (int i = x - 1; i <= x + 1; i++)
{
for (int j = y - 1; j <= y + 1; j++)
{
for (int k = z - 1; k <= z + 1; k++)
{
if (image->inNarrowBounds(i, j, k) && image->getVoxel(i, j, k) > 0 && res_image->getVoxel(i, j, k) == 0)
{
candidates.insert(triple(i, j, k));
}
}
}
}
}
triple::triple(int x, int y, int z)
{
this->x = x;
this->y = y;
this->z = z;
}
bool triple::operator==(triple that) const
{
return this->x == that.x && this->y == that.y && this->z == that.z;
}
int triple::hash() const
{
return (701 * x + y) * 877 + z;
}