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Fixed issues with ImagePyramidRenderer and SegmentationRenderer when used with RenderToImage #201

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Fixed issues with ImagePyramidRenderer and SegmentationRenderer when used with RenderToImage #201

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191 changes: 99 additions & 92 deletions source/FAST/Visualization/ImagePyramidRenderer/ImagePyramidRenderer.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -76,15 +76,88 @@ void ImagePyramidRenderer::loadAttributes() {
setSharpening(getBooleanAttribute("sharpening"));
}

void
ImagePyramidRenderer::draw(Matrix4f perspectiveMatrix, Matrix4f viewingMatrix, float zNear, float zFar, bool mode2D,
int viewWidth,
int viewHeight) {
int ImagePyramidRenderer::loadTileTexture(std::string tileID) {
// Check if tile has been processed before
if(mTexturesToRender.count(tileID) > 0)
return -1;

//std::cout << "Loading tile " << tileID << " queue size: " << m_tileQueue.size() << std::endl;

// Create texture
auto parts = split(tileID, "_");
if(parts.size() != 3)
throw Exception("incorrect tile format");

int level = std::stoi(parts[0]);
int tile_x = std::stoi(parts[1]);
int tile_y = std::stoi(parts[2]);
//std::cout << "Creating texture for tile " << tile_x << " " << tile_y << " at level " << level << std::endl;
Image::pointer tile;
{
auto access = m_input->getAccess(ACCESS_READ);
try {
tile = access->getPatchAsImage(level, tile_x, tile_y, false);
} catch(Exception &e) {
//reportWarning() << "Error occured while trying to open patch " << tile_x << " " << tile_y << reportEnd();
// Tile was missing, just skip it..
std::lock_guard<std::mutex> lock(m_tileQueueMutex);
mTexturesToRender[tileID] = 0;
return -1;
}
if(m_postProcessingSharpening) {
m_sharpening->setInputData(tile);
tile = m_sharpening->updateAndGetOutputData<Image>();
}
}
auto tileAccess = tile->getImageAccess(ACCESS_READ);
// Copy data from CPU to GL texture
GLuint textureID;
glGenTextures(1, &textureID);
glBindTexture(GL_TEXTURE_2D, textureID);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_LINEAR);

// TODO Why is this needed:
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_CLAMP_TO_EDGE);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_CLAMP_TO_EDGE);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_R, GL_CLAMP_TO_EDGE);

// WSI data from openslide is stored as ARGB, need to handle this here: BGRA and reverse
if(m_input->isBGRA()) {
glTexImage2D(GL_TEXTURE_2D, 0, GL_COMPRESSED_RGBA, tile->getWidth(), tile->getHeight(), 0, GL_BGRA,
GL_UNSIGNED_BYTE,
tileAccess->get());
} else {
if(tile->getNrOfChannels() == 3) {
glTexImage2D(GL_TEXTURE_2D, 0, GL_COMPRESSED_RGB, tile->getWidth(), tile->getHeight(), 0, GL_RGB,
GL_UNSIGNED_BYTE,
tileAccess->get());
} else if(tile->getNrOfChannels() == 4) {
glTexImage2D(GL_TEXTURE_2D, 0, GL_COMPRESSED_RGBA, tile->getWidth(), tile->getHeight(), 0, GL_RGBA,
GL_UNSIGNED_BYTE,
tileAccess->get());
}
}
GLint compressedImageSize = 0;
glGetTexLevelParameteriv(GL_TEXTURE_2D, 0, GL_TEXTURE_COMPRESSED_IMAGE_SIZE, &compressedImageSize);
glBindTexture(GL_TEXTURE_2D, 0);
glFinish(); // Make sure texture is done before adding it

{
std::lock_guard<std::mutex> lock(m_tileQueueMutex);
mTexturesToRender[tileID] = textureID;
}
return compressedImageSize;
}

void ImagePyramidRenderer::draw(Matrix4f perspectiveMatrix, Matrix4f viewingMatrix, float zNear, float zFar, bool mode2D,
int viewWidth,
int viewHeight) {
auto dataToRender = getDataToRender();
if(dataToRender.empty())
return;

if(!m_bufferThread) {
if(!m_bufferThread && m_view != nullptr) {
// Create thread to load patches
// Create a GL context for the thread which is sharing with the context of the view
auto context = new QGLContext(View::getGLFormat(), m_view);
Expand Down Expand Up @@ -139,77 +212,7 @@ ImagePyramidRenderer::draw(Matrix4f perspectiveMatrix, Matrix4f viewingMatrix, f
m_tileQueue.pop_back();
}

// Check if tile has been processed before
if(mTexturesToRender.count(tileID) > 0)
continue;

//std::cout << "Loading tile " << tileID << " queue size: " << m_tileQueue.size() << std::endl;

// Create texture
auto parts = split(tileID, "_");
if(parts.size() != 3)
throw Exception("incorrect tile format");

int level = std::stoi(parts[0]);
int tile_x = std::stoi(parts[1]);
int tile_y = std::stoi(parts[2]);
//std::cout << "Creating texture for tile " << tile_x << " " << tile_y << " at level " << level << std::endl;
Image::pointer tile;
{
auto access = m_input->getAccess(ACCESS_READ);
try {
tile = access->getPatchAsImage(level, tile_x, tile_y, false);
} catch(Exception &e) {
//reportWarning() << "Error occured while trying to open patch " << tile_x << " " << tile_y << reportEnd();
// Tile was missing, just skip it..
std::lock_guard<std::mutex> lock(m_tileQueueMutex);
mTexturesToRender[tileID] = 0;
continue;
}
if(m_postProcessingSharpening) {
m_sharpening->setInputData(tile);
tile = m_sharpening->updateAndGetOutputData<Image>();
}
}
auto tileAccess = tile->getImageAccess(ACCESS_READ);
// Copy data from CPU to GL texture
GLuint textureID;
glGenTextures(1, &textureID);
glBindTexture(GL_TEXTURE_2D, textureID);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_LINEAR);

// TODO Why is this needed:
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_CLAMP_TO_EDGE);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_CLAMP_TO_EDGE);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_R, GL_CLAMP_TO_EDGE);

// WSI data from openslide is stored as ARGB, need to handle this here: BGRA and reverse
if(m_input->isBGRA()) {
glTexImage2D(GL_TEXTURE_2D, 0, GL_COMPRESSED_RGBA, tile->getWidth(), tile->getHeight(), 0, GL_BGRA,
GL_UNSIGNED_BYTE,
tileAccess->get());
} else {
if(tile->getNrOfChannels() == 3) {
glTexImage2D(GL_TEXTURE_2D, 0, GL_COMPRESSED_RGB, tile->getWidth(), tile->getHeight(), 0, GL_RGB,
GL_UNSIGNED_BYTE,
tileAccess->get());
} else if(tile->getNrOfChannels() == 4) {
glTexImage2D(GL_TEXTURE_2D, 0, GL_COMPRESSED_RGBA, tile->getWidth(), tile->getHeight(), 0, GL_RGBA,
GL_UNSIGNED_BYTE,
tileAccess->get());
}
}
GLint compressedImageSize = 0;
glGetTexLevelParameteriv(GL_TEXTURE_2D, 0, GL_TEXTURE_COMPRESSED_IMAGE_SIZE, &compressedImageSize);
glBindTexture(GL_TEXTURE_2D, 0);
glFinish(); // Make sure texture is done before adding it

{
std::lock_guard<std::mutex> lock(m_tileQueueMutex);
mTexturesToRender[tileID] = textureID;
}
memoryUsage += compressedImageSize;
memoryUsage += loadTileTexture(tileID);
//std::cout << "Texture cache in ImagePyramidRenderer using " << (float)memoryUsage / (1024 * 1024) << " MB" << std::endl;
}
});
Expand Down Expand Up @@ -251,7 +254,7 @@ ImagePyramidRenderer::draw(Matrix4f perspectiveMatrix, Matrix4f viewingMatrix, f
float percentageShownX = (float)width / fullWidth;
float percentageShownY = (float)height / fullHeight;
// With current level, do we have have enough pixels to fill the view?
if(percentageShownX * levelWidth > m_view->width() && percentageShownY * levelHeight > m_view->height()) {
if(percentageShownX * levelWidth > viewWidth && percentageShownY * levelHeight > viewHeight) {
// If yes, stop here
levelToUse = level;
break;
Expand Down Expand Up @@ -337,26 +340,30 @@ ImagePyramidRenderer::draw(Matrix4f perspectiveMatrix, Matrix4f viewingMatrix, f
))
continue;


// Is patch in cache?
bool textureReady = false;
uint textureID;
{
std::lock_guard<std::mutex> lock(m_tileQueueMutex);
textureReady = mTexturesToRender.count(tileString) > 0;
}
if(!textureReady) {
// Add to queue if not in cache
if(m_view != nullptr) {
// Is patch in cache?
bool textureReady = false;
{
std::lock_guard<std::mutex> lock(m_tileQueueMutex);
// Remove any duplicates first
m_tileQueue.remove(tileString); // O(n) time complexity..
m_tileQueue.push_back(tileString);
//std::cout << "Added tile " << tileString << " to queue" << std::endl;
textureReady = mTexturesToRender.count(tileString) > 0;
}
if(!textureReady) {
// Add to queue if not in cache
{
std::lock_guard<std::mutex> lock(m_tileQueueMutex);
// Remove any duplicates first
m_tileQueue.remove(tileString); // O(n) time complexity..
m_tileQueue.push_back(tileString);
//std::cout << "Added tile " << tileString << " to queue" << std::endl;
}
m_queueEmptyCondition.notify_one();
continue;
} else {
textureID = mTexturesToRender[tileString];
}
m_queueEmptyCondition.notify_one();
continue;
} else {
int bytes = loadTileTexture(tileString);
textureID = mTexturesToRender[tileString];
}

Expand Down
1 change: 1 addition & 0 deletions source/FAST/Visualization/ImagePyramidRenderer/ImagePyramidRenderer.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,7 @@ class FAST_EXPORT ImagePyramidRenderer : public Renderer {
std::shared_ptr<ImagePyramid> m_input;

void drawTextures(Matrix4f &perspectiveMatrix, Matrix4f &viewingMatrix, bool mode2D);
int loadTileTexture(std::string tileID);
};

}
43 changes: 43 additions & 0 deletions source/FAST/Visualization/RenderToImage/Tests.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,12 @@
#include <FAST/Visualization/VolumeRenderer/MaximumIntensityProjection.hpp>
#include <FAST/Visualization/SliceRenderer/SliceRenderer.hpp>
#include <FAST/Visualization/VolumeRenderer/ThresholdVolumeRenderer.hpp>
#include <FAST/Visualization/ImagePyramidRenderer/ImagePyramidRenderer.hpp>
#include <FAST/Importers/WholeSlideImageImporter.hpp>
#include <FAST/Algorithms/ImagePatch/PatchGenerator.hpp>
#include <FAST/Algorithms/TissueSegmentation/TissueSegmentation.hpp>
#include <FAST/Algorithms/ImagePatch/PatchStitcher.hpp>
#include <FAST/Algorithms/RunUntilFinished/RunUntilFinished.hpp>

using namespace fast;

Expand Down Expand Up @@ -83,3 +89,40 @@ TEST_CASE("RenderToImage 3D geom", "[fast][RenderToImage]") {
auto toImage = RenderToImage::create(Color::White(), 1024 )->connect(renderer2);
ImageExporter::create("test_render_to_image_3d_geom.png")->connect(toImage)->run();
}
TEST_CASE("RenderToImage image pyramid", "[fast][RenderToImage]") {
auto importer = WholeSlideImageImporter::create(Config::getTestDataPath() + "/WSI/CMU-1.svs");

auto renderer = ImagePyramidRenderer::create()->connect(importer);

auto toImage = RenderToImage::create()->connect(renderer);
auto image = toImage->runAndGetOutputData<Image>();

//auto renderer2 = ImageRenderer::create()->connect(image);
//SimpleWindow2D::create()->connect(renderer2)->run();

ImageExporter::create("test_render_to_image_image_pyramid.png")->connect(image)->run();
}

TEST_CASE("RenderToImage image pyramid + segmentation", "[fast][RenderToImage]") {
auto importer = WholeSlideImageImporter::create(Config::getTestDataPath() + "/WSI/CMU-1.svs");

auto generator = PatchGenerator::create(512, 512, 1, 1)->connect(importer);

auto segmentation = TissueSegmentation::create()->connect(generator);

auto stitcher = PatchStitcher::create()->connect(segmentation);

auto finish = RunUntilFinished::create()->connect(stitcher);

auto renderer = ImagePyramidRenderer::create()->connect(importer);

auto renderer2 = SegmentationRenderer::create()->connect(finish);

auto toImage = RenderToImage::create()->connect({renderer, renderer2});
auto image = toImage->runAndGetOutputData<Image>();

//auto renderer3 = ImageRenderer::create()->connect(image);
//SimpleWindow2D::create()->connect(renderer3)->run();

ImageExporter::create("test_render_to_image_image_pyramid_and_segmentation.png")->connect(image)->run();
}
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