Showing content from https://raw.githubusercontent.com/michalsta/opentims/master/examples/get_data.cpp below:
// A small example demonstrating the basic usage of OpenTIMS in C++. // Edit to fill in the path to your TIMS data directory (below), // then compile by issuing the "make" command. #include #include #include #include "../opentims++/opentims_all.cpp" int main(int argc, char** argv) { /* Setup: parse args, set up paths */ std::string data_path; std::string bruker_binary_lib_path; bool use_bruker_code = false; if(argc==2) { use_bruker_code = false; data_path = argv[1]; } else if(argc==3) { use_bruker_code = true; bruker_binary_lib_path = argv[1]; data_path = argv[2]; } else { std::cerr << "Usage:" << std::endl; std::cerr << std::endl; std::cerr << "\t" << argv[0] << " " << std::endl; std::cerr << "This will NOT use Bruker's proprietary conversion functions" << std::endl; std::cerr << std::endl; std::cerr << "or:" << std::endl; std::cerr << std::endl; std::cerr << "\t" << argv[0] << " " << std::endl; std::cerr << "to use Bruker's conversion functions" << std::endl; std::cerr << std::endl; return 1; } // If we're using Bruker's proprietary conversion functions, they must be set up before opening any TimsDataHandle(s) that will use them if(use_bruker_code) { DefaultTof2MzConverterFactory::setAsDefault (bruker_binary_lib_path.c_str()); DefaultScan2InvIonMobilityConverterFactory::setAsDefault (bruker_binary_lib_path.c_str()); } // Open the dataset TimsDataHandle TDH(data_path); // Allocate buffers for data: instead of reallocating for every frame, we just allocate a buffer that will fit all // and reuse it. const size_t buffer_size_needed = TDH.max_peaks_in_frame(); std::unique_ptr frame_ids = std::make_unique (buffer_size_needed); std::unique_ptr scan_ids = std::make_unique (buffer_size_needed); std::unique_ptr tofs = std::make_unique (buffer_size_needed); std::unique_ptr intensities = std::make_unique (buffer_size_needed); std::unique_ptr mzs = use_bruker_code ? std::make_unique (buffer_size_needed) : nullptr; std::unique_ptr inv_ion_mobilities = use_bruker_code ? std::make_unique (buffer_size_needed) : nullptr; std::unique_ptr retention_times = std::make_unique (buffer_size_needed); // Print table header std::cout << "\"Frame ID\"" << "\t" << "\"Scan ID\"" << "\t" << "\"Time-of-flight\"" << "\t" << "\"Intensity\"" << "\t"; if(use_bruker_code) std::cout << "\"MZ\"" << "\t" << "\"Inverse of ion mobility\"" << "\t"; std::cout << "\"Retention time\"" << std::endl; // Obtain frames: as a map frame_id -> frame object std::unordered_map & frame_desc = TDH.get_frame_descs(); // Iterate over frames (in order), and output a CSV-formatted data dump for(uint32_t idx = TDH.min_frame_id(); idx < TDH.max_frame_id(); idx++) // The file format in theory allows some frames to be missing - we have not seen any such files in the wild though if(TDH.has_frame(idx)) { TimsFrame& frame = TDH.get_frame(idx); frame.save_to_buffs(frame_ids.get(), scan_ids.get(), tofs.get(), intensities.get(), mzs.get(), inv_ion_mobilities.get(), retention_times.get()); for(size_t peak_id = 0; peak_id < frame.num_peaks; peak_id++) { std::cout << frame_ids[peak_id] << "\t" << scan_ids[peak_id] << "\t" << tofs[peak_id] << "\t" << intensities[peak_id] << "\t"; if(use_bruker_code) std::cout << mzs[peak_id] << "\t" << inv_ion_mobilities[peak_id] << "\t"; std::cout << retention_times[peak_id] << std::endl; } } }
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