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main.cpp
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#include <libxml/parser.h>
#include <libxml/xmlschemas.h>
#include <libxml/xmlmemory.h>
#include <libxml/debugXML.h>
#include <libxml/HTMLtree.h>
#include <libxml/xmlIO.h>
#include <libxml/xinclude.h>
#include <libxml/catalog.h>
#include <libxslt/xslt.h>
#include <libxslt/xsltInternals.h>
#include <libxslt/transform.h>
#include <libxslt/xsltutils.h>
#include <boost/make_shared.hpp>
#include "siemensraw.h"
#include "base64.h"
#include "XNode.h"
#include "ConverterXml.h"
#include "ismrmrd/ismrmrd.h"
#include "ismrmrd/dataset.h"
#include "ismrmrd/version.h"
#include "ismrmrd/xml.h"
#include "converter_version.h"
#include <boost/program_options.hpp>
namespace po = boost::program_options;
#include <boost/locale/encoding_utf.hpp>
using boost::locale::conv::utf_to_utf;
#include <iomanip>
#include <iostream>
#include <string>
#include <fstream>
#include <sstream>
#include <streambuf>
#include <utility>
#include <typeinfo>
const size_t MYSTERY_BYTES_EXPECTED = 160;
// defined in generated defaults.cpp
extern void initializeEmbeddedFiles(void);
extern std::map<std::string, std::string> global_embedded_files;
struct ChannelHeaderAndData
{
sChannelHeader header;
std::vector<complex_float_t> data;
};
struct MeasurementHeaderBuffer
{
std::string name;
std::string buf;
};
void calc_vds(double slewmax,double gradmax,double Tgsample,double Tdsample,int Ninterleaves,
double* fov, int numfov,double krmax,
int ngmax, double** xgrad,double** ygrad,int* numgrad);
void calc_traj(double* xgrad, double* ygrad, int ngrad, int Nints, double Tgsamp, double krmax,
double** x_trajectory, double** y_trajectory,
double** weights);
std::vector<ISMRMRD::Waveform> readSyncdata(std::ifstream &siemens_dat, bool VBFILE, unsigned long acquisitions,
uint32_t dma_length, sScanHeader scanheader, ISMRMRD::IsmrmrdHeader &header,
long scan_counter);
std::string getparammap_file_content(const std::string ¶mmap_file, const std::string &usermap_file, bool VBFILE);
std::vector<MrParcRaidFileEntry>
readParcFileEntries(std::ifstream &siemens_dat, const MrParcRaidFileHeader &ParcRaidHead, bool VBFILE);
std::vector<MeasurementHeaderBuffer> readMeasurementHeaderBuffers(std::ifstream &siemens_dat, uint32_t num_buffers);
std::string readXmlConfig(bool debug_xml, const std::string ¶mmap_file_content, uint32_t num_buffers,
std::vector<MeasurementHeaderBuffer> &buffers, std::vector<std::string> &wip_double,
Trajectory &trajectory, long &dwell_time_0, long &max_channels, long &radial_views, long* global_table_pos,
std::string &baseLine_string, std::string &protocol_name, std::string& software_version);
std::string parseXML(bool debug_xml, const std::string ¶mmap_xsl_content, std::string &schema_file_name_content,
const std::string xml_config);
ISMRMRD::NDArray<float>
getTrajectory(const std::vector<std::string> &wip_double, const Trajectory &trajectory, long dwell_time_0,
long radial_views);
ISMRMRD::Acquisition
getAcquisition(bool flash_pat_ref_scan, const Trajectory &trajectory, long dwell_time_0, long* global_table_pos, long max_channels,
bool isAdjustCoilSens, bool isAdjQuietCoilSens, bool isVB, ISMRMRD::NDArray<float> &traj,
const sScanHeader &scanhead, const std::vector<ChannelHeaderAndData> &channels);
void readScanHeader(std::ifstream &siemens_dat, bool VBFILE, sMDH &mdh, sScanHeader &scanhead);
std::vector<ChannelHeaderAndData>
readChannelHeaders(std::ifstream &siemens_dat, bool VBFILE, const sScanHeader &scanhead);
int xml_file_is_valid(std::string &xml, std::string &schema_file) {
xmlDocPtr doc;
//parse an XML in-memory block and build a tree.
doc = xmlParseMemory(xml.c_str(), xml.size());
xmlDocPtr schema_doc;
//parse an XML in-memory block and build a tree.
schema_doc = xmlParseMemory(schema_file.c_str(), schema_file.size());
//Create an XML Schemas parse context for that document. NB. The document may be modified during the parsing process.
xmlSchemaParserCtxtPtr parser_ctxt = xmlSchemaNewDocParserCtxt(schema_doc);
if (parser_ctxt == NULL) {
/* unable to create a parser context for the schema */
xmlFreeDoc(schema_doc);
return -2;
}
//parse a schema definition resource and build an internal XML Shema struture which can be used to validate instances.
xmlSchemaPtr schema = xmlSchemaParse(parser_ctxt);
if (schema == NULL) {
/* the schema itself is not valid */
xmlSchemaFreeParserCtxt(parser_ctxt);
xmlFreeDoc(schema_doc);
return -3;
}
//Create an XML Schemas validation context based on the given schema.
xmlSchemaValidCtxtPtr valid_ctxt = xmlSchemaNewValidCtxt(schema);
if (valid_ctxt == NULL) {
/* unable to create a validation context for the schema */
xmlSchemaFree(schema);
xmlSchemaFreeParserCtxt(parser_ctxt);
xmlFreeDoc(schema_doc);
xmlFreeDoc(doc);
return -4;
}
//Validate a document tree in memory. Takes a schema validation context and a parsed document tree
int is_valid = (xmlSchemaValidateDoc(valid_ctxt, doc) == 0);
xmlSchemaFreeValidCtxt(valid_ctxt);
xmlSchemaFree(schema);
xmlSchemaFreeParserCtxt(parser_ctxt);
xmlFreeDoc(schema_doc);
xmlFreeDoc(doc);
/* force the return value to be non-negative on success */
return is_valid ? 1 : 0;
}
std::string get_date_time_string() {
time_t rawtime;
struct tm *timeinfo;
time(&rawtime);
timeinfo = localtime(&rawtime);
std::stringstream str;
str << timeinfo->tm_year + 1900 << "-"
<< std::setw(2) << std::setfill('0') << timeinfo->tm_mon + 1
<< "-"
<< std::setw(2) << std::setfill('0') << timeinfo->tm_mday
<< " "
<< std::setw(2) << std::setfill('0') << timeinfo->tm_hour
<< ":"
<< std::setw(2) << std::setfill('0') << timeinfo->tm_min
<< ":"
<< std::setw(2) << std::setfill('0') << timeinfo->tm_sec;
std::string ret = str.str();
return ret;
}
bool is_number(const std::string &s) {
bool ret = true;
for (unsigned int i = 0; i < s.size(); i++) {
if (!std::isdigit(s.c_str()[i])) {
ret = false;
break;
}
}
return ret;
}
std::string get_time_string(size_t hours, size_t mins, size_t secs) {
std::stringstream str;
str << std::setw(2) << std::setfill('0') << hours << ":"
<< std::setw(2) << std::setfill('0') << mins << ":"
<< std::setw(2) << std::setfill('0') << secs;
std::string ret = str.str();
return ret;
}
bool fill_ismrmrd_header(ISMRMRD::IsmrmrdHeader &h, const std::string &study_date, const std::string &study_time) {
try {
// ---------------------------------
// fill more info into the ismrmrd header
// ---------------------------------
// study
bool study_date_needed = false;
bool study_time_needed = false;
if (h.studyInformation) {
if (!h.studyInformation->studyDate) {
study_date_needed = true;
}
if (!h.studyInformation->studyTime) {
study_time_needed = true;
}
} else {
study_date_needed = true;
study_time_needed = true;
}
if (study_date_needed || study_time_needed) {
ISMRMRD::StudyInformation study;
if(h.studyInformation)
study = *h.studyInformation;
if(study_date_needed && !study_date.empty())
{
study.studyDate.set(study_date);
std::cout << "Study date: " << study_date << std::endl;
}
if (study_time_needed && !study_time.empty()) {
study.studyTime.set(study_time);
std::cout << "Study time: " << study_time << std::endl;
}
h.studyInformation.set(study);
}
// ---------------------------------
// go back to string
// ---------------------------------
}
catch (...) {
return false;
}
return true;
}
void append_buffers_to_xml_header(std::vector<MeasurementHeaderBuffer> &buffers, size_t num_buffers,
ISMRMRD::IsmrmrdHeader &header) {
for (unsigned int b = 0; b < num_buffers; b++) {
ISMRMRD::UserParameterString p;
p.value = base64_encode(reinterpret_cast<const unsigned char *>(buffers[b].buf.c_str()), buffers[b].buf.size());
p.name = std::string("SiemensBuffer_") + buffers[b].name;
if (!header.userParameters.is_present()) {
ISMRMRD::UserParameters up;
header.userParameters = up;
}
header.userParameters().userParameterBase64.push_back(p);
}
}
std::string ProcessParameterMap(const XProtocol::XNode &node, const char *mapfile) {
TiXmlDocument out_doc;
TiXmlDeclaration *decl = new TiXmlDeclaration("1.0", "", "");
out_doc.LinkEndChild(decl);
ConverterXMLNode out_n(&out_doc);
//Input document
TiXmlDocument doc;
doc.Parse(mapfile);
TiXmlHandle docHandle(&doc);
TiXmlElement *parameters = docHandle.FirstChildElement("siemens").FirstChildElement("parameters").ToElement();
if (parameters) {
TiXmlNode *p = 0;
while ((p = parameters->IterateChildren("p", p))) {
TiXmlHandle ph(p);
TiXmlText *s = ph.FirstChildElement("s").FirstChild().ToText();
TiXmlText *d = ph.FirstChildElement("d").FirstChild().ToText();
if (s && d) {
std::string source = s->Value();
std::string destination = d->Value();
std::vector<std::string> split_path;
boost::split(split_path, source, boost::is_any_of("."), boost::token_compress_on);
if (is_number(split_path[0])) {
std::cout << "First element of path (" << source << ") cannot be numeric" << std::endl;
continue;
}
std::string search_path = split_path[0];
for (unsigned int i = 1; i < split_path.size() - 1; i++) {
/*
if (is_number(split_path[i]) && (i != split_path.size())) {
std::cout << "Numeric index not supported inside path for source = " << source << std::endl;
continue;
}*/
search_path += std::string(".") + split_path[i];
}
int index = -1;
if (is_number(split_path[split_path.size() - 1])) {
index = atoi(split_path[split_path.size() - 1].c_str());
} else {
search_path += std::string(".") + split_path[split_path.size() - 1];
}
const XProtocol::XNode *n = boost::apply_visitor(XProtocol::getChildNodeByName(search_path), node);
std::vector<std::string> parameters;
if (n) {
parameters = boost::apply_visitor(XProtocol::getStringValueArray(), *n);
} else {
std::cout << "Search path: " << search_path << " not found." << std::endl;
}
if (index >= 0) {
if (parameters.size() > index) {
out_n.add(destination, parameters[index]);
} else {
std::cout << "Parameter index (" << index << ") not valid for search path " << search_path
<< std::endl;
continue;
}
} else {
out_n.add(destination, parameters);
}
} else {
std::cout << "Malformed parameter map" << std::endl;
}
}
} else {
std::cout << "Malformed parameter map (parameters section not found)" << std::endl;
return std::string("");
}
return XmlToString(out_doc);
}
/// compute noise dwell time in us for dependency and built-in noise in VD/VB lines
double compute_noise_sample_in_us(size_t num_of_noise_samples_this_acq, bool isAdjustCoilSens, bool isAdjQuietCoilSens,
bool isVB) {
if (isAdjustCoilSens) {
return 5.0;
} else if (isAdjQuietCoilSens) {
return 4.0;
} else if (isVB) {
return (1e6 / num_of_noise_samples_this_acq / 130.0);
} else {
return (((long) (76800.0 / num_of_noise_samples_this_acq)) / 10.0);
}
return 5.0;
}
std::string load_embedded(std::string name) {
std::string contents;
std::map<std::string, std::string>::iterator it = global_embedded_files.find(name);
if (it != global_embedded_files.end()) {
std::string encoded = it->second;
contents = base64_decode(encoded);
} else {
std::stringstream sstream;
sstream << "ERROR: File " << name << " is not embedded!";
throw std::runtime_error(sstream.str());
}
return contents;
}
std::string ws2s(const std::wstring &wstr) {
std::string ret(wstr.size(), '0');
for (size_t i = 0; i < wstr.size(); i++) {
wchar_t c = wstr[i];
if (((uint32_t) c) > 127) {
ret[i] = 'X';
} else {
ret[i] = static_cast<char>(c);
}
}
return ret;
}
int main(int argc, char* argv[]) {
std::string siemens_dat_filename;
unsigned int measurement_number;
std::string parammap_file;
std::string parammap_xsl;
std::string usermap_file;
std::string usermap_xsl;
std::string schema_file_name;
std::string ismrmrd_file;
std::string ismrmrd_group;
std::string date_time = get_date_time_string();
std::string study_date_user_supplied;
bool debug_xml = false;
bool flash_pat_ref_scan = false;
bool header_only = false;
bool append_buffers = false;
bool list = false;
std::string to_extract;
std::string xslt_home;
po::options_description desc("Allowed options");
desc.add_options()
("help,h", "Produce HELP message")
("version,v", "Prints converter version and ISMRMRD version")
("file,f", po::value<std::string>(&siemens_dat_filename), "<SIEMENS dat file>")
("measNum,z", po::value<unsigned int>(&measurement_number)->default_value(1), "<Measurement number>")
("pMap,m", po::value<std::string>(¶mmap_file), "<Parameter map XML file>")
("pMapStyle,x", po::value<std::string>(¶mmap_xsl), "<Parameter stylesheet XSL file>")
("user-map", po::value<std::string>(&usermap_file), "<Provide a parameter map XML file>")
("user-stylesheet", po::value<std::string>(&usermap_xsl), "<Provide a parameter stylesheet XSL file>")
("output,o", po::value<std::string>(&ismrmrd_file)->default_value("output.h5"), "<ISMRMRD output file>")
("outputGroup,g", po::value<std::string>(&ismrmrd_group)->default_value("dataset"),
"<ISMRMRD output group>")
("list,l", po::value<bool>(&list)->implicit_value(true), "<List embedded files>")
("extract,e", po::value<std::string>(&to_extract), "<Extract embedded file>")
("debug,X", po::value<bool>(&debug_xml)->implicit_value(true), "<Debug XML flag>")
("flashPatRef,F", po::value<bool>(&flash_pat_ref_scan)->implicit_value(true), "<FLASH PAT REF flag>")
("headerOnly,H", po::value<bool>(&header_only)->implicit_value(true),
"<HEADER ONLY flag (create xml header only)>")
("bufferAppend,B", po::value<bool>(&append_buffers)->implicit_value(true),
"<Append Siemens protocol buffers (bas64) to user parameters>")
("studyDate", po::value<std::string>(&study_date_user_supplied),
"<User can supply study date, in the format of yyyy-mm-dd>");
po::options_description display_options("Allowed options");
display_options.add_options()
("help,h", "Produce HELP message")
("version,v", "Prints converter version and ISMRMRD version")
("file,f", "<SIEMENS dat file>")
("measNum,z", "<Measurement number>")
("pMap,m", "<Parameter map XML>")
("pMapStyle,x", "<Parameter stylesheet XSL>")
("user-map", "<Provide a parameter map XML file>")
("user-stylesheet", "<Provide a parameter stylesheet XSL file>")
("output,o", "<ISMRMRD output file>")
("outputGroup,g", "<ISMRMRD output group>")
("list,l", "<List embedded files>")
("extract,e", "<Extract embedded file>")
("debug,X", "<Debug XML flag>")
("flashPatRef,F", "<FLASH PAT REF flag>")
("headerOnly,H", "<HEADER ONLY flag (create xml header only)>")
("bufferAppend,B", "<Append protocol buffers>")
("studyDate", "<User can supply study date, in the format of yyyy-mm-dd>");
po::variables_map vm;
try {
po::store(po::parse_command_line(argc, argv, desc), vm);
po::notify(vm);
if (vm.count("help")) {
std::cout << display_options << "\n";
return 1;
}
if (vm.count("version")) {
std::cout << "Converter version is: " << SIEMENS_TO_ISMRMRD_VERSION_MAJOR << "."
<< SIEMENS_TO_ISMRMRD_VERSION_MINOR << "." << SIEMENS_TO_ISMRMRD_VERSION_PATCH << "\n";
std::cout << "Built against ISMRMRD version: " << ISMRMRD_VERSION_MAJOR << "." << ISMRMRD_VERSION_MINOR
<< "." << ISMRMRD_VERSION_PATCH << "\n";
return 1;
}
}
catch (po::error& e) {
std::cerr << "ERROR: " << e.what() << std::endl << std::endl;
std::cerr << display_options << std::endl;
return -1;
}
// Add all embedded files to the global_embedded_files map
initializeEmbeddedFiles();
// List embededded parameter maps if requested
if (list) {
std::map<std::string, std::string>::iterator iter;
std::cout << "Embedded Files: " << std::endl;
for (iter = global_embedded_files.begin(); iter != global_embedded_files.end(); ++iter) {
if (iter->first != "ismrmrd.xsd") {
std::cout << " " << iter->first << std::endl;
}
}
return 0;
}
// Extract specified parameter map if requested
if (to_extract.length() > 0) {
std::string contents = load_embedded(to_extract);
std::ofstream outfile(to_extract.c_str());
outfile.write(contents.c_str(), contents.size());
std::cout << to_extract << " successfully extracted. " << std::endl;
return 0;
}
if (measurement_number < 1) {
std::cerr << "The measurement number must be a positive integer" << std::endl;
std::cerr << display_options << "\n";
return -1;
}
// Siemens file must be specified
if (siemens_dat_filename.length() == 0) {
std::cerr << "Missing Siemens DAT filename" << std::endl;
std::cerr << display_options << "\n";
return -1;
}
// Check if Siemens file is valid
std::ifstream infile(siemens_dat_filename.c_str());
if (!infile) {
std::cerr << "Provided Siemens file can not be open or does not exist." << std::endl;
std::cerr << display_options << "\n";
return -1;
}
std::cout << "Siemens file is: " << siemens_dat_filename << std::endl;
std::string schema_file_name_content = load_embedded("ismrmrd.xsd");
std::ifstream siemens_dat(siemens_dat_filename.c_str(), std::ios::binary);
MrParcRaidFileHeader ParcRaidHead;
siemens_dat.read((char*)(&ParcRaidHead), sizeof(MrParcRaidFileHeader));
bool VBFILE = false;
if (ParcRaidHead.hdSize_ > 32) {
VBFILE = true;
//Rewind, we have no raid file header.
siemens_dat.seekg(0, std::ios::beg);
ParcRaidHead.hdSize_ = ParcRaidHead.count_;
ParcRaidHead.count_ = 1;
}
else if (ParcRaidHead.hdSize_ != 0) {
//This is a VB line data file
std::cerr << "Only VD line files with MrParcRaidFileHeader.hdSize_ == 0 (MR_PARC_RAID_ALLDATA) supported."
<< std::endl;
return -1;
}
if (!VBFILE && measurement_number > ParcRaidHead.count_) {
std::cout << "The file you are trying to convert has only " << ParcRaidHead.count_ << " measurements."
<< std::endl;
std::cout << "You are trying to convert measurement number: " << measurement_number << std::endl;
return -1;
}
//if it is a VB scan
if (VBFILE && measurement_number != 1) {
std::cout << "The file you are trying to convert is a VB file and it has only one measurement." << std::endl;
std::cout << "You tried to convert measurement number: " << measurement_number << std::endl;
return -1;
}
std::string parammap_file_content = getparammap_file_content(parammap_file, usermap_file, VBFILE);
std::cout << "This file contains " << ParcRaidHead.count_ << " measurement(s)." << std::endl;
std::vector<MrParcRaidFileEntry> ParcFileEntries = readParcFileEntries(siemens_dat, ParcRaidHead, VBFILE);
// find the beginning of the desired measurement
siemens_dat.seekg(ParcFileEntries[measurement_number - 1].off_, std::ios::beg);
uint32_t dma_length = 0, num_buffers = 0;
siemens_dat.read((char*)(&dma_length), sizeof(uint32_t));
siemens_dat.read((char*)(&num_buffers), sizeof(uint32_t));
//std::cout << "Measurement header DMA length: " << mhead.dma_length << std::endl;
auto buffers = readMeasurementHeaderBuffers(siemens_dat, num_buffers);
//We need to be on a 32 byte boundary after reading the buffers
long long int position_in_meas =
(long long int) (siemens_dat.tellg()) - ParcFileEntries[measurement_number - 1].off_;
if (position_in_meas % 32 != 0) {
siemens_dat.seekg(32 - (position_in_meas % 32), std::ios::cur);
}
// Measurement header done!
//Now we should have the measurement headers, so let's use the Meas header to create the XML parametersstd::string xml_config;
std::vector<std::string> wip_double;
Trajectory trajectory;
long dwell_time_0;
long max_channels;
long radial_views;
long* global_table_pos = new long[3];
std::string baseLineString;
std::string protocol_name;
std::string software_version;
std::string xml_config = readXmlConfig(debug_xml, parammap_file_content, num_buffers, buffers, wip_double,
trajectory, dwell_time_0,
max_channels, radial_views, global_table_pos, baseLineString, protocol_name, software_version);
// whether this scan is a adjustment scan
bool isAdjustCoilSens = false;
if (protocol_name == "AdjCoilSens") {
isAdjustCoilSens = true;
}
bool isAdjQuietCoilSens = false;
if (protocol_name == "AdjQuietCoilSens") {
isAdjQuietCoilSens = true;
}
// whether this scan is from VB line
bool isVB = false;
if ((baseLineString.find("VB17") != std::string::npos)
|| (baseLineString.find("VB15") != std::string::npos)
|| (baseLineString.find("VB13") != std::string::npos)
|| (baseLineString.find("VB11") != std::string::npos)) {
isVB = true;
}
std::cout << "Baseline: " << baseLineString << std::endl;
std::cout << "Software version: " << software_version << std::endl;
bool isNX = false;
if ((baseLineString.find("NXVA") != std::string::npos) || (software_version.find("XA11") != std::string::npos) )
{
isNX = true;
}
if (debug_xml) {
std::ofstream o("xml_raw.xml");
o.write(xml_config.c_str(), xml_config.size());
}
std::string parammap_xsl_content;
if (parammap_xsl.length() == 0) {
// If the user did not specify any stylesheet
if (usermap_xsl.length() == 0) {
if (isNX)
{
parammap_xsl_content = load_embedded("IsmrmrdParameterMap_Siemens_NX.xsl");
std::cout << "Parameter XSL stylesheet is: IsmrmrdParameterMap_Siemens_NX.xsl" << std::endl;
}
else
{
parammap_xsl_content = load_embedded("IsmrmrdParameterMap_Siemens.xsl");
std::cout << "Parameter XSL stylesheet is: IsmrmrdParameterMap_Siemens.xsl" << std::endl;
}
}
// If the user specified only a user-supplied stylesheet
else {
std::ifstream f(usermap_xsl.c_str());
if (!f) {
std::cerr << "Parameter XSL stylesheet: " << usermap_xsl << " does not exist." << std::endl;
return -1;
}
std::cout << "Parameter XSL stylesheet is: " << usermap_xsl << std::endl;
std::string str_f((std::istreambuf_iterator<char>(f)), std::istreambuf_iterator<char>());
parammap_xsl_content = str_f;
}
}
else {
// If the user specified both an embedded and user-supplied stylesheet
if (usermap_xsl.length() > 0) {
std::cerr << "Cannot specify a user-supplied parameter map XSL stylesheet AND embedded stylesheet"
<< std::endl;
return -1;
}
// The user specified an embedded stylesheet only
parammap_xsl_content = load_embedded(parammap_xsl);
std::cout << "Parameter XSL stylesheet is: " << parammap_xsl << std::endl;
}
ISMRMRD::IsmrmrdHeader header;
{
std::string config = parseXML(debug_xml, parammap_xsl_content, schema_file_name_content, xml_config);
ISMRMRD::deserialize(config.c_str(), header);
}
//Append buffers to xml_config if requested
if (append_buffers) {
append_buffers_to_xml_header(buffers, num_buffers, header);
}
// Free memory used for MeasurementHeaderBuffers
auto ismrmrd_dataset = boost::make_shared<ISMRMRD::Dataset>(ismrmrd_file.c_str(), ismrmrd_group.c_str(), true);
//If this is a spiral acquisition, we will calculate the trajectory and add it to the individual profilesISMRMRD::NDArray<float> traj;
auto traj = getTrajectory(wip_double, trajectory, dwell_time_0, radial_views);
uint32_t last_mask = 0;
unsigned long int acquisitions = 1;
unsigned long int sync_data_packets = 0;
sMDH mdh;//For VB line
bool first_call = true;
while (!(last_mask & 1) && //Last scan not encountered
(((ParcFileEntries[measurement_number - 1].off_ + ParcFileEntries[measurement_number - 1].len_) -
siemens_dat.tellg()) > sizeof(sScanHeader))) //not reached end of measurement without acqend
{
size_t position_in_meas = siemens_dat.tellg();
sScanHeader scanhead;
readScanHeader(siemens_dat, VBFILE, mdh, scanhead);
if (!siemens_dat) {
std::cerr << "Error reading header at acquisition " << acquisitions << "." << std::endl;
break;
}
uint32_t dma_length = scanhead.ulFlagsAndDMALength & MDH_DMA_LENGTH_MASK;
uint32_t mdh_enable_flags = scanhead.ulFlagsAndDMALength & MDH_ENABLE_FLAGS_MASK;
//Check if this is synch data, if so, it must be handled differently.
if (scanhead.aulEvalInfoMask[0] & (1 << 5)) {
uint32_t last_scan_counter = acquisitions - 1;
auto waveforms = readSyncdata(siemens_dat, VBFILE, acquisitions, dma_length, scanhead, header,
last_scan_counter);
for (auto &w : waveforms)
ismrmrd_dataset->appendWaveform(w);
sync_data_packets++;
continue;
}
if (first_call) {
uint32_t time_stamp = scanhead.ulTimeStamp;
// convert to acqusition date and time
double timeInSeconds = time_stamp * 2.5 / 1e3;
size_t hours = (size_t) (timeInSeconds / 3600);
size_t mins = (size_t) ((timeInSeconds - hours * 3600) / 60);
size_t secs = (size_t) (timeInSeconds - hours * 3600 - mins * 60);
hours = hours % 24;
mins = mins % 60;
std::string study_time = get_time_string(hours, mins, secs);
// if some of the ismrmrd header fields are not filled, here is a place to take some further actions
if (!fill_ismrmrd_header(header, study_date_user_supplied, study_time)) {
std::cerr << "Failed to further fill XML header" << std::endl;
}
std::stringstream sstream;
ISMRMRD::serialize(header, sstream);
xml_config = sstream.str();
if (xml_file_is_valid(xml_config, schema_file_name_content) <= 0) {
std::cerr << "Generated XML is not valid according to the ISMRMRD schema" << std::endl;
return -1;
}
if (debug_xml) {
std::ofstream o("processed.xml");
o.write(xml_config.c_str(), xml_config.size());
}
//This means we should only create XML header and exit
if (header_only) {
std::ofstream header_out_file(ismrmrd_file.c_str());
header_out_file << xml_config;
return -1;
}
// Create an ISMRMRD dataset
}
//This check only makes sense in VD line files.
if (!VBFILE && (scanhead.lMeasUID != ParcFileEntries[measurement_number - 1].measId_)) {
//Something must have gone terribly wrong. Bail out.
if (first_call) {
std::cerr << "Corrupted or retro-recon dataset detected (scanhead.lMeasUID != ParcFileEntries["
<< measurement_number - 1 << "].measId_)" << std::endl;
std::cerr << "Fix the scanhead.lMeasUID ... " << std::endl;
}
scanhead.lMeasUID = ParcFileEntries[measurement_number - 1].measId_;
}
if (first_call) first_call = false;
//Allocate data for channels
std::vector<ChannelHeaderAndData> channels = readChannelHeaders(siemens_dat, VBFILE, scanhead);
if (!siemens_dat) {
std::cerr << "Error reading data at acquisition " << acquisitions << "." << std::endl;
break;
}
acquisitions++;
last_mask = scanhead.aulEvalInfoMask[0];
if (scanhead.aulEvalInfoMask[0] & 1) {
std::cout << "Last scan reached..." << std::endl;
break;
}
ismrmrd_dataset->appendAcquisition(
getAcquisition(flash_pat_ref_scan, trajectory, dwell_time_0, global_table_pos, max_channels, isAdjustCoilSens,
isAdjQuietCoilSens, isVB, traj, scanhead, channels));
}//End of the while loop
delete [] global_table_pos;
if (!siemens_dat) {
std::cerr << "WARNING: Unexpected error. Please check the result." << std::endl;
return -1;
}
ismrmrd_dataset->writeHeader(xml_config);
//Mystery bytes. There seems to be 160 mystery bytes at the end of the data.
std::streamoff mystery_bytes = (std::streamoff) (ParcFileEntries[measurement_number - 1].off_ +
ParcFileEntries[measurement_number - 1].len_) -
siemens_dat.tellg();
if (mystery_bytes > 0) {
if (mystery_bytes != MYSTERY_BYTES_EXPECTED) {
// Something in not quite right
std::cerr << "WARNING: Unexpected number of mystery bytes detected: " << mystery_bytes << std::endl;
std::cerr << "ParcFileEntries[" << measurement_number - 1 << "].off_ = "
<< ParcFileEntries[measurement_number - 1].off_ << std::endl;
std::cerr << "ParcFileEntries[" << measurement_number - 1 << "].len_ = "
<< ParcFileEntries[measurement_number - 1].len_ << std::endl;
std::cerr << "siemens_dat.tellg() = " << siemens_dat.tellg() << std::endl;
std::cerr << "Please check the result." << std::endl;
} else {
// Read the mystery bytes
char mystery_data[MYSTERY_BYTES_EXPECTED];
siemens_dat.read(reinterpret_cast<char *>(&mystery_data), mystery_bytes);
//After this we have to be on a 512 byte boundary
if (siemens_dat.tellg() % 512) {
siemens_dat.seekg(512 - (siemens_dat.tellg() % 512), std::ios::cur);
}
}
}
size_t end_position = siemens_dat.tellg();
siemens_dat.seekg(0, std::ios::end);
size_t eof_position = siemens_dat.tellg();
if (end_position != eof_position && ParcRaidHead.count_ == measurement_number) {
size_t additional_bytes = eof_position - end_position;
std::cerr << "WARNING: End of file was not reached during conversion. There are " <<
additional_bytes << " additional bytes at the end of file." << std::endl;
}
return 0;
}
std::vector<ChannelHeaderAndData>
readChannelHeaders(std::ifstream &siemens_dat, bool VBFILE, const sScanHeader &scanhead) {
size_t nchannels = scanhead.ushUsedChannels;
auto channels = std::vector<ChannelHeaderAndData>(nchannels);
sMDH mdh;
for (unsigned int c = 0; c < nchannels; c++) {
if (VBFILE) {
if (c > 0) {
siemens_dat.read(reinterpret_cast<char *>(&mdh), sizeof(sMDH));
}
channels[c].header.ulTypeAndChannelLength = 0;
channels[c].header.lMeasUID = mdh.lMeasUID;
channels[c].header.ulScanCounter = mdh.ulScanCounter;
channels[c].header.ulReserved1 = 0;
channels[c].header.ulSequenceTime = 0;
channels[c].header.ulUnused2 = 0;
channels[c].header.ulChannelId = mdh.ushChannelId;
channels[c].header.ulUnused3 = 0;
channels[c].header.ulCRC = 0;
} else {
siemens_dat.read(reinterpret_cast<char *>(&channels[c].header), sizeof(sChannelHeader));
}
size_t nsamples = scanhead.ushSamplesInScan;
channels[c].data = std::vector<complex_float_t>(nsamples);
siemens_dat.read(reinterpret_cast<char *>(&channels[c].data[0]), nsamples * sizeof(complex_float_t));
}
return channels;
}
void readScanHeader(std::ifstream &siemens_dat, bool VBFILE, sMDH &mdh, sScanHeader &scanhead) {
siemens_dat.read(reinterpret_cast<char *>(&scanhead.ulFlagsAndDMALength), sizeof(uint32_t));
if (VBFILE) {
siemens_dat.read(reinterpret_cast<char *>(&mdh) + sizeof(uint32_t), sizeof(sMDH) - sizeof(uint32_t));
scanhead.lMeasUID = mdh.lMeasUID;
scanhead.ulScanCounter = mdh.ulScanCounter;
scanhead.ulTimeStamp = mdh.ulTimeStamp;
scanhead.ulPMUTimeStamp = mdh.ulPMUTimeStamp;
scanhead.ushSystemType = 0;
scanhead.ulPTABPosDelay = 0;
scanhead.lPTABPosX = 0;
scanhead.lPTABPosY = 0;
scanhead.lPTABPosZ = mdh.ushPTABPosNeg;//TODO: Modify calculation
scanhead.ulReserved1 = 0;
scanhead.aulEvalInfoMask[0] = mdh.aulEvalInfoMask[0];
scanhead.aulEvalInfoMask[1] = mdh.aulEvalInfoMask[1];
scanhead.ushSamplesInScan = mdh.ushSamplesInScan;
scanhead.ushUsedChannels = mdh.ushUsedChannels;
scanhead.sLC = mdh.sLC;
scanhead.sCutOff = mdh.sCutOff;
scanhead.ushKSpaceCentreColumn = mdh.ushKSpaceCentreColumn;
scanhead.ushCoilSelect = mdh.ushCoilSelect;
scanhead.fReadOutOffcentre = mdh.fReadOutOffcentre;
scanhead.ulTimeSinceLastRF = mdh.ulTimeSinceLastRF;
scanhead.ushKSpaceCentreLineNo = mdh.ushKSpaceCentreLineNo;
scanhead.ushKSpaceCentrePartitionNo = mdh.ushKSpaceCentrePartitionNo;
scanhead.sSliceData = mdh.sSliceData;
memset(scanhead.aushIceProgramPara, 0, sizeof(uint16_t) * 24);
memcpy(scanhead.aushIceProgramPara, mdh.aushIceProgramPara, 8 * sizeof(uint16_t));
memset(scanhead.aushReservedPara, 0, sizeof(uint16_t) * 4);
scanhead.ushApplicationCounter = 0;
scanhead.ushApplicationMask = 0;
scanhead.ulCRC = 0;
} else {
siemens_dat.read(reinterpret_cast<char *>(&scanhead) + sizeof(uint32_t),
sizeof(sScanHeader) - sizeof(uint32_t));
}
}
ISMRMRD::Acquisition
getAcquisition(bool flash_pat_ref_scan, const Trajectory &trajectory, long dwell_time_0, long* global_table_pos, long max_channels,
bool isAdjustCoilSens, bool isAdjQuietCoilSens, bool isVB, ISMRMRD::NDArray<float> &traj,
const sScanHeader &scanhead, const std::vector<ChannelHeaderAndData> &channels) {
ISMRMRD::Acquisition ismrmrd_acq;
// The number of samples, channels and trajectory dimensions is set below
// Acquisition header values are zero by default
ismrmrd_acq.measurement_uid() = scanhead.lMeasUID;
ismrmrd_acq.scan_counter() = scanhead.ulScanCounter;
ismrmrd_acq.acquisition_time_stamp() = scanhead.ulTimeStamp;
ismrmrd_acq.physiology_time_stamp()[0] = scanhead.ulPMUTimeStamp;
ismrmrd_acq.available_channels() = (uint16_t) max_channels;
// uint64_t channel_mask[16]; //Mask to indicate which channels are active. Support for 1024 channels
ismrmrd_acq.discard_pre() = scanhead.sCutOff.ushPre;
ismrmrd_acq.discard_post() = scanhead.sCutOff.ushPost;
ismrmrd_acq.center_sample() = scanhead.ushKSpaceCentreColumn;
// std::cout << "isAdjustCoilSens, isVB : " << isAdjustCoilSens << " " << isVB << std::endl;
if (scanhead.aulEvalInfoMask[0] & (1ULL << 25)) { //This is noise
ismrmrd_acq.sample_time_us() = compute_noise_sample_in_us(scanhead.ushSamplesInScan, isAdjustCoilSens,
isAdjQuietCoilSens, isVB);
} else {
ismrmrd_acq.sample_time_us() = dwell_time_0 / 1000.0f;
}
// std::cout << "ismrmrd_acq.sample_time_us(): " << ismrmrd_acq.sample_time_us() << std::endl;
ismrmrd_acq.position()[0] = scanhead.sSliceData.sSlicePosVec.flSag + (float) (global_table_pos[0]);
ismrmrd_acq.position()[1] = scanhead.sSliceData.sSlicePosVec.flCor + (float) (global_table_pos[1]);
ismrmrd_acq.position()[2] = scanhead.sSliceData.sSlicePosVec.flTra + (float) (global_table_pos[2]);
// Convert Siemens quaternions to direction cosines.
// In the Siemens convention the quaternion corresponds to a rotation matrix with columns P R S
// Siemens stores the quaternion as (W,X,Y,Z)
float quat[4];
quat[0] = scanhead.sSliceData.aflQuaternion[1]; // X
quat[1] = scanhead.sSliceData.aflQuaternion[2]; // Y
quat[2] = scanhead.sSliceData.aflQuaternion[3]; // Z
quat[3] = scanhead.sSliceData.aflQuaternion[0]; // W
ISMRMRD::ismrmrd_quaternion_to_directions(quat,
ismrmrd_acq.phase_dir(),
ismrmrd_acq.read_dir(),
ismrmrd_acq.slice_dir());
//std::cout << "scanhead.ulScanCounter = " << scanhead.ulScanCounter << std::endl;
//std::cout << "quat = [" << quat[0] << " " << quat[1] << " " << quat[2] << " " << quat[3] << "]" << std::endl;
//std::cout << "phase_dir = [" << ismrmrd_acq.phase_dir()[0] << " " << ismrmrd_acq.phase_dir()[1] << " " << ismrmrd_acq.phase_dir()[2] << "]" << std::endl;
//std::cout << "read_dir = [" << ismrmrd_acq.read_dir()[0] << " " << ismrmrd_acq.read_dir()[1] << " " << ismrmrd_acq.read_dir()[2] << "]" << std::endl;
//std::cout << "slice_dir = [" << ismrmrd_acq.slice_dir()[0] << " " << ismrmrd_acq.slice_dir()[1] << " " << ismrmrd_acq.slice_dir()[2] << "]" << std::endl;
//std::cout << "--------------------------------------------------------" << std::endl;
ismrmrd_acq.patient_table_position()[0] = (float) scanhead.lPTABPosX;
ismrmrd_acq.patient_table_position()[1] = (float) scanhead.lPTABPosY;
ismrmrd_acq.patient_table_position()[2] = (float) scanhead.lPTABPosZ;