Implemented ImagePyramidAccess:setBlankPatch

source/FAST/Data/Access/ImagePyramidAccess.cpp

@@ -522,6 +522,19 @@ void jpegErrorExit(j_common_ptr cinfo) {
 }
 
 int ImagePyramidAccess::readTileFromTIFF(void *data, int x, int y, int level) {
+    const auto tileWidth = m_image->getLevelTileWidth(level);
+    const auto tileHeight = m_image->getLevelTileHeight(level);
+    const auto channels = m_image->getNrOfChannels();
+    TIFFSetDirectory(m_tiffHandle, level);
+    uint32_t tile_id = TIFFComputeTile(m_tiffHandle, x, y, 0, 0);
+    if(TIFFGetStrileByteCount(m_tiffHandle, tile_id) == 1) { // Blank patch
+        if(channels == 1) {
+            std::memset(data, 0, tileWidth*tileHeight*channels);
+        } else {
+            std::memset(data, 255, tileWidth*tileHeight*channels);
+        }
+        return 0;
+    }
     // Assumes level (directory is already set)
     if(m_compressionFormat == ImageCompression::NEURAL_NETWORK) {
         auto decompressionModel = m_image->getDecompressionModel();
@@ -531,7 +544,6 @@ int ImagePyramidAccess::readTileFromTIFF(void *data, int x, int y, int level) {
         shape[0] = 1;
         int64_t size = shape.getTotalSize()*4;
         float* buffer = new float[shape.getTotalSize()];
-        uint32_t tile_id = TIFFComputeTile(m_tiffHandle, x, y, 0, 0);
         int bytesRead = TIFFReadRawTile(m_tiffHandle, tile_id, buffer, size);
         auto tensor = Tensor::create(buffer, shape);
         decompressionModel->connect(tensor);
@@ -548,11 +560,7 @@ int ImagePyramidAccess::readTileFromTIFF(void *data, int x, int y, int level) {
         int bytesRead = 0;
         if(m_compressionFormat == ImageCompression::JPEG) {
             // Use libjpeg for decompression, as ome-tiff files doesn't seem to like tiff's internal jpeg
-            auto tileWidth = m_image->getLevelTileWidth(level);
-            auto tileHeight = m_image->getLevelTileHeight(level);
-            const auto channels = m_image->getNrOfChannels();
             auto buffer = make_uninitialized_unique<char[]>(tileWidth*tileHeight*channels);
-            uint32_t tile_id = TIFFComputeTile(m_tiffHandle, x, y, 0, 0);
             bytesRead = TIFFReadRawTile(m_tiffHandle, tile_id, buffer.get(), tileWidth*tileHeight*channels);
 
             jpeg_decompress_struct cinfo;
@@ -582,11 +590,7 @@ int ImagePyramidAccess::readTileFromTIFF(void *data, int x, int y, int level) {
                 throw Exception("JPEG error: " + std::string(e.what())); // or return an error code
             }
         } else if(m_compressionFormat == ImageCompression::JPEGXL) {
-            auto tileWidth = m_image->getLevelTileWidth(level);
-            auto tileHeight = m_image->getLevelTileHeight(level);
-            const auto channels = m_image->getNrOfChannels();
             auto buffer = make_uninitialized_unique<char[]>(tileWidth*tileHeight*channels);
-            uint32_t tile_id = TIFFComputeTile(m_tiffHandle, x, y, 0, 0);
             bytesRead = TIFFReadRawTile(m_tiffHandle, tile_id, buffer.get(), tileWidth*tileHeight*channels);
 
             JPEGXLCompression jxl;
@@ -604,5 +608,20 @@ void ImagePyramidAccess::setTIFFDirectory(int level) {
         TIFFSetDirectory(m_tiffHandle, level);
 }
 
+void ImagePyramidAccess::setBlankPatch(int level, int x, int y) {
+    if(m_tiffHandle == nullptr)
+        throw Exception("setBlankPatch only available for TIFF backend ImagePyramids");
+
+    std::lock_guard<std::mutex> lock(m_readMutex);
+    TIFFSetDirectory(m_tiffHandle, level);
+    uint32_t tile_id = TIFFComputeTile(m_tiffHandle, x, y, 0, 0);
+    TIFFSetWriteOffset(m_tiffHandle, 0); // Set write offset to 0, so that we dont appen data
+    // Writing zero bytes, will produce a warning, thus we write 1 byte
+    char data = 0;
+    TIFFWriteRawTile(m_tiffHandle, tile_id, &data, 1);
+    TIFFCheckpointDirectory(m_tiffHandle);
+    m_initializedPatchList.insert(std::to_string(level) + "-" + std::to_string(tile_id));
+}
+
 
 }

source/FAST/Data/Access/ImagePyramidAccess.hpp

@@ -63,6 +63,7 @@ class FAST_EXPORT ImagePyramidAccess : Object {
 	typedef std::unique_ptr<ImagePyramidAccess> pointer;
 	ImagePyramidAccess(std::vector<ImagePyramidLevel> levels, openslide_t* fileHandle, TIFF* tiffHandle, std::shared_ptr<ImagePyramid> imagePyramid, bool writeAccess, std::unordered_set<std::string>& initializedPatchList, std::mutex& readMutex, ImageCompression compressionFormat);
 	void setPatch(int level, int x, int y, std::shared_ptr<Image> patch, bool propagate = true);
+	void setBlankPatch(int level, int x, int y);
 	bool isPatchInitialized(uint level, uint x, uint y);
 	template <class T>
 	std::unique_ptr<T[]> getPatchData(int level, int x, int y, int width, int height);

source/FAST/Data/ImagePyramid.cpp

@@ -148,6 +148,7 @@ ImagePyramid::ImagePyramid(int width, int height, int channels, int patchWidth,
         // TODO need to initialize somehow?
         // We need to write the first tile for some reason... or we will get an error saying it is missing required
         // TileOffsets
+        TIFFCheckpointDirectory(m_tiffHandle); // Need to check in the tile width and length tags, before writing a tile
         if(m_compressionFormat == ImageCompression::JPEGXL) {
             auto data = std::make_unique<uchar[]>(samplesPerPixel); // Is initialized to zeros
             auto tileID = TIFFComputeTile(tiff, 0, 0, 0, 0);
@@ -166,9 +167,9 @@ ImagePyramid::ImagePyramid(int width, int height, int channels, int patchWidth,
 		}*/
         // END
 
+        TIFFWriteDirectory(m_tiffHandle);
 		reportInfo() << "Done creating level " << currentLevel << reportEnd();
 		++currentLevel;
-		TIFFWriteDirectory(m_tiffHandle);
     }
 
     mBoundingBox = DataBoundingBox(Vector3f(getFullWidth(), getFullHeight(), 0));