From d8019e99d7991c60775aeabf10b9a32a83df3281 Mon Sep 17 00:00:00 2001
From: Erik Smistad <ersmistad@gmail.com>
Date: Fri, 22 Nov 2024 15:46:17 +0100
Subject: [PATCH] Fixed some minor issues in previous commit

---
 source/FAST/Data/Access/ImagePyramidAccess.cpp |  7 +------
 source/FAST/Data/Access/ImagePyramidAccess.hpp | 15 ++++++++++++++-
 source/FAST/Data/ImagePyramid.cpp              |  9 +++++----
 3 files changed, 20 insertions(+), 11 deletions(-)

diff --git a/source/FAST/Data/Access/ImagePyramidAccess.cpp b/source/FAST/Data/Access/ImagePyramidAccess.cpp
index 0301540e2..817b19cf5 100644
--- a/source/FAST/Data/Access/ImagePyramidAccess.cpp
+++ b/source/FAST/Data/Access/ImagePyramidAccess.cpp
@@ -351,7 +351,7 @@ uint32_t ImagePyramidAccess::writeTileToTIFF(int level, int x, int y, uchar *dat
 
 uint32_t ImagePyramidAccess::writeTileToTIFFJPEGXL(int level, int x, int y, uchar *data) {
     std::lock_guard<std::mutex> lock(m_readMutex);
-    setTIFFDirectory(level);
+    TIFFSetDirectory(m_tiffHandle, level);
     uint32_t tile_id = TIFFComputeTile(m_tiffHandle, x, y, 0, 0);
     JPEGXLCompression jxl;
     std::vector<uchar> compressed;
@@ -603,11 +603,6 @@ int ImagePyramidAccess::readTileFromTIFF(void *data, int x, int y, int level) {
     }
 }
 
-void ImagePyramidAccess::setTIFFDirectory(int level) {
-    if(TIFFCurrentDirectory(m_tiffHandle) != 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");
diff --git a/source/FAST/Data/Access/ImagePyramidAccess.hpp b/source/FAST/Data/Access/ImagePyramidAccess.hpp
index 05ff26a33..71b38e964 100644
--- a/source/FAST/Data/Access/ImagePyramidAccess.hpp
+++ b/source/FAST/Data/Access/ImagePyramidAccess.hpp
@@ -62,7 +62,21 @@ class FAST_EXPORT ImagePyramidAccess : Object {
 public:
 	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);
+	/**
+	 * @brief Write a patch to the pyramid
+	 * @param level
+	 * @param x
+	 * @param y
+	 * @param patch
+	 * @param propagate
+	 */
 	void setPatch(int level, int x, int y, std::shared_ptr<Image> patch, bool propagate = true);
+	/**
+	 * @brief Write patch/tile as empty. It will render as white/black
+	 * @param level
+	 * @param x
+	 * @param y
+	 */
 	void setBlankPatch(int level, int x, int y);
 	bool isPatchInitialized(uint level, uint x, uint y);
 	template <class T>
@@ -99,7 +113,6 @@ class FAST_EXPORT ImagePyramidAccess : Object {
     uint32_t writeTileToTIFFJPEGXL(int level, int x, int y, uchar *data);
     uint32_t writeTileToTIFFNeuralNetwork(int level, int x, int y, std::shared_ptr<Image> image);
     int readTileFromTIFF(void* data, int x, int y, int level);
-    void setTIFFDirectory(int level);
 };
 
 template <class T>
diff --git a/source/FAST/Data/ImagePyramid.cpp b/source/FAST/Data/ImagePyramid.cpp
index bbe51b377..2c810909e 100644
--- a/source/FAST/Data/ImagePyramid.cpp
+++ b/source/FAST/Data/ImagePyramid.cpp
@@ -150,10 +150,11 @@ ImagePyramid::ImagePyramid(int width, int height, int channels, int patchWidth,
         // 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);
-            TIFFSetWriteOffset(tiff, 0); // Set write offset to 0, so that we dont appen data
-            TIFFWriteRawTile(tiff, tileID, data.get(), samplesPerPixel);
+            // TODO Not needed?
+            //auto data = std::make_unique<uchar[]>(samplesPerPixel); // Is initialized to zeros
+            //auto tileID = TIFFComputeTile(tiff, 0, 0, 0, 0);
+            //TIFFSetWriteOffset(tiff, 0); // Set write offset to 0, so that we dont appen data
+            //TIFFWriteRawTile(tiff, tileID, data.get(), samplesPerPixel);
         } else {
             auto data = std::make_unique<uchar[]>(levelData.tileWidth*levelData.tileHeight*samplesPerPixel); // Is initialized to zeros
             TIFFWriteTile(tiff, data.get(), 0, 0, 0, 0);