#include "PixelariumCzi.hpp" #include #include #include #include #include #include #include #include "ILog.hpp" #include "libCZI.h" #include "libCZI_Pixels.h" namespace { bool comp_blockinfo_params(const pixelarium::imaging::CziParams& params, const libCZI::SubBlockInfo& info) { bool res{true}; info.coordinate.EnumValidDimensions( [&](libCZI::DimensionIndex dim, int start) -> bool { if (params.dimension_map.at(dim) == start) { return true; } res &= false; return true; }); return res; } constexpr int try_get_index_match(const pixelarium::imaging::CziParams& params, libCZI::ICZIReader& reader) { int index{-1}; reader.EnumerateSubBlocks( [&](int idx, const libCZI::SubBlockInfo& info) -> bool { if (comp_blockinfo_params(params, info)) { index = idx; // returning false will stop the enumeration return false; } return true; }); return index; } } // namespace std::optional CZISubBlockToCvMat(std::shared_ptr bitmap, libCZI::PixelType pixeltype, const pixelarium::utils::log::ILog& log) { const auto cv_pixel = GetCVPixelTypeAndSize(pixeltype); // ToDo(MAK): fix this makeshift pixel-type-catch if (cv_pixel.size < 0 || cv_pixel.size > 4) return std::nullopt; log.Info(std::format("{}: source pixel type {}, target cv pixel type {}, pixel size {}", __PRETTY_FUNCTION__, static_cast(pixeltype), cv_pixel.type, cv_pixel.size)); size_t height{bitmap->GetHeight()}; size_t width{bitmap->GetWidth()}; auto fill_mat = cv::Mat(height, width, cv_pixel.type); if (const auto bitmap_info = bitmap->Lock(); bitmap_info.ptrDataRoi) { for (size_t h{0}; h < height; ++h) { unsigned char* source_row = ((unsigned char*)bitmap_info.ptrDataRoi) + bitmap_info.stride * h; unsigned char* target_row = fill_mat.ptr(h); for (size_t w{0}; w < width; ++w) { switch (cv_pixel.size) { case 1: target_row[w] = source_row[w]; break; case 2: reinterpret_cast(target_row)[w] = reinterpret_cast(source_row)[w]; break; case 3: target_row[3 * w] = source_row[3 * w]; target_row[3 * w + 1] = source_row[3 * w + 1]; target_row[3 * w + 2] = source_row[3 * w + 2]; break; case 4: reinterpret_cast(target_row)[w] = reinterpret_cast(source_row)[w]; break; default: throw std::runtime_error("Unknown pixel type requested!"); break; } } } } // this is outside of the previous if-clause on purpose: // no matter if we reach the inner scope of this clause, we locked the bitmap, // so here it has to be unlocked. bitmap->Unlock(); return fill_mat; } std::optional pixelarium::imaging::PixelariumCzi::SubblockToCvMat(int index) { log_.Info(std::format("{}: constructing bitmap with index {}", __PRETTY_FUNCTION__, index)); auto block = this->czi_reader_->ReadSubBlock(index); auto bitmap = block->CreateBitmap(); return CZISubBlockToCvMat(bitmap, block->GetSubBlockInfo().pixelType, log_); } pixelarium::imaging::PixelariumCzi::PixelariumCzi(const std::string& uri, const Log& log) : log_(log) { if (!std::filesystem::exists(uri)) { throw std::runtime_error("Render file not found."); } this->is_empty_ = false; this->uri_ = std::filesystem::path(uri); auto stream = libCZI::CreateStreamFromFile(this->uri_.wstring().c_str()); this->czi_reader_ = libCZI::CreateCZIReader(); this->czi_reader_->Open(stream); this->image_statistics_ = this->czi_reader_->GetStatistics(); this->image_statistics_.dimBounds.EnumValidDimensions( [&](libCZI::DimensionIndex dim, int start, int) -> bool { this->dimension_map_[dim] = start; return true; }); } std::optional pixelarium::imaging::PixelariumCzi::TryGetImage() { return SubblockToCvMat(0); } std::optional pixelarium::imaging::PixelariumCzi::TryGetImage(const IImageQuery& query) { const auto czi_query = static_cast(query); int index = try_get_index_match(czi_query, *this->czi_reader_); if (index < 0) { return SubblockToCvMat(0); } return SubblockToCvMat(index); }