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refactored xsyg.cpp
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Simplifications, whitespace changes,
fixed some typos in metadata (lexStuidoVersion, simulator -> stimulator).
The only real change is that a detector="Spectrometer" file was converted
to a number of y columns, all with the same title "cts [1/ch]".
Now the number preceding the y values is used as the title.
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@wojdyr
wojdyr committed Sep 8, 2020
1 parent 9e01d79 commit 60609da
Showing 1 changed file with 95 additions and 262 deletions.
357 changes: 95 additions & 262 deletions xylib/xsyg.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -21,291 +21,124 @@ const FormatInfo XsygDataSet::fmt_info(
"xsyg",
"Freiberg Instruments (FI) Lexsyg",
"xsyg",
false, // whether binary
false, // whether binary
true, // whether has multi-blocks
&XsygDataSet::ctor,
&XsygDataSet::check
);

bool XsygDataSet::check(std::istream &f, string*)
{

ptree tree;
read_xml(f, tree);

//check if child "Sample" is part of the XML file
if(tree.count("Sample") == 0 ){
return false;
} else {
return true;
}

return tree.count("Sample") != 0;
}

void XsygDataSet::load_data(std::istream &f, const char*) {

ptree tree;
unsigned int measurement_nr, AQ_nr = 1;

//read XML file
read_xml(f, tree);

ptree sample = tree.get_child("Sample");

//store metaData

std::string state, parentID, name, user, startDate, sampleCarrier, lexsygID, lexStudioVersion, firmwareVersion,
os, comment;

state = sample.get("<xmlattr>.state","");
parentID = sample.get("<xmlattr>.parentID","");
name = sample.get("<xmlattr>.name","");
user = sample.get("<xmlattr>.user","");
startDate = sample.get("<xmlattr>.startDate","");
sampleCarrier = sample.get("<xmlattr>.sampleCarrier","");
lexsygID = sample.get("<xmlattr>.lexsygID","");
lexStudioVersion = sample.get("<xmlattr>.lexStudioVersion","");
firmwareVersion = sample.get("<xmlattr>.firmwareVersion","");
os = sample.get("<xmlattr>.os","");
comment = sample.get("<xmlattr>.comment","");

meta["state"] = state;
meta["parentID"] = parentID;
meta["name"] = name;
meta["user"] = user;
meta["StartDate"] = startDate;
meta["sampleCarrier"] = sampleCarrier;
meta["lexsygID"] = lexsygID;
meta["lexStuidoVersion"] = lexStudioVersion;
meta["firmwareVersion"] = firmwareVersion;
meta["os"] = os;
meta["comment"] = comment;

//loop Aliquots
meta["state"] = sample.get("<xmlattr>.state", "");
meta["name"] = sample.get("<xmlattr>.name", "");
meta["user"] = sample.get("<xmlattr>.user", "");
meta["startDate"] = sample.get("<xmlattr>.startDate", "");
meta["sampleCarrier"] = sample.get("<xmlattr>.sampleCarrier", "");
meta["lexsygID"] = sample.get("<xmlattr>.lexsygID", "");
meta["lexStudioVersion"] = sample.get("<xmlattr>.lexStudioVersion", "");
meta["firmwareVersion"] = sample.get("<xmlattr>.firmwareVersion", "");
meta["os"] = sample.get("<xmlattr>.os", "");
meta["comment"] = sample.get("<xmlattr>.comment", "");

int AQ_nr = 0;
std::pair<ptiter, ptiter> sequenceRange = sample.equal_range("Sequence");

for (ptiter it_seq = sequenceRange.first; it_seq != sequenceRange.second; ++it_seq, ++AQ_nr) {

std::pair<ptiter, ptiter> recordRange = it_seq->second.equal_range("Record");

//set counter = 0
measurement_nr = 0;

//loop Measurements
for (ptiter i = recordRange.first; i != recordRange.second; ++i) {

std::pair<ptiter, ptiter> curveRange = i->second.equal_range("Curve");

//loop Curves
for (ptiter j = curveRange.first; j != curveRange.second; ++j) {

if(j -> second.get("<xmlattr>.curveType","") == "measured"){

if(j -> second.get("<xmlattr>.detector","") != ""){

if(j -> second.get("<xmlattr>.detector","") != "Spectrometer"){

++measurement_nr;

//create new Block, x- and y-axis
Block *blk = new Block;
VecColumn *x_axis_col = new VecColumn;
VecColumn *y_axis_col = new VecColumn;

//read data between <Curve> ... </Curve>
std::string data = j->second.data();

std::istringstream ss(data);
std::string token, token2;

//set counter 0 for decision if x- or y-axis
int it_data = 0;

while(std::getline(ss, token, ';')) {

std::istringstream ss2(token);

while(std::getline(ss2, token2, ',')) {

it_data++;

//take every second element as y-value
if(it_data %2 == 1){
x_axis_col-> add_values_from_str(token2);
} else {
y_axis_col-> add_values_from_str(token2);
}

}// end 2nd while-loop: token 2
}// end 1st while-loop: token


//extract meta data
string curveDescriptor = j -> second.get("<xmlattr>.curveDescripter","");
std::vector<std::string> curve_descriptor_split;
boost::split(curve_descriptor_split, curveDescriptor, boost::is_any_of(";"));

string recordType = i -> second.get("<xmlattr>.recordType","");
string detector = j -> second.get("<xmlattr>.detector","");
string state = j -> second.get("<xmlattr>.state","");
string parentID = j-> second.get("<xmlattr>.state","");
string startDate = j -> second.get("<xmlattr>.startDate","");
string curveType = j -> second.get("<xmlattr>.curveType","");
string stimulator = j -> second.get("<xmlattr>.simulator","");
string offset= j -> second.get("<xmlattr>.offset","");

//add meta data
blk->meta["state"] = state;
blk->meta["parentID"] = parentID;
blk->meta["detector"] = detector;
blk->meta["startDate"] = startDate;
blk->meta["curveType"] = curveType;
blk->meta["stimulator"] = stimulator;
blk->meta["curveDescriptor"] = curveDescriptor;
blk->meta["offset"] = offset;


//set names of columns
x_axis_col-> set_name(curve_descriptor_split[0]);
y_axis_col-> set_name(curve_descriptor_split[1]);

//set name of block
ostringstream convert_AQ, convert_measurement_nr;
convert_AQ << AQ_nr;
convert_measurement_nr << measurement_nr;

blk->set_name("AQ: " + convert_AQ.str() + ", Meas.: " +
convert_measurement_nr.str() + ", Type: " + recordType + " (" + detector +")");

// add column to block
blk->add_column(x_axis_col);
blk->add_column(y_axis_col);

//finally: add block
add_block(blk);

} else { // end if not spectrometer

++measurement_nr;

//create new Block, x- and y-axis
Block *blk = new Block;
VecColumn *x_axis_col = new VecColumn;

//read wavelength from attribute "wavelengthTable"
std::string wavelength = j->second.get("<xmlattr>.wavelengthTable","");
std::istringstream wavelength_ss(wavelength);
std::string wavelength_split;

while(std::getline(wavelength_ss, wavelength_split, ';')) {
x_axis_col-> add_values_from_str(wavelength_split);
for (ptiter it_seq = sequenceRange.first; it_seq != sequenceRange.second; ++it_seq) {
++AQ_nr;
std::pair<ptiter, ptiter> recordRange = it_seq->second.equal_range("Record");
int measurement_nr = 0;
//loop Measurements
for (ptiter i = recordRange.first; i != recordRange.second; ++i) {
std::pair<ptiter, ptiter> curveRange = i->second.equal_range("Curve");
string recordType = i->second.get("<xmlattr>.recordType", "");
//loop Curves
for (ptiter j = curveRange.first; j != curveRange.second; ++j) {
if (j->second.get("<xmlattr>.curveType", "") != "measured")
continue;
if (j->second.get("<xmlattr>.detector", "") == "")
continue;
Block *blk = new Block;
++measurement_nr;
string curveDesc = j->second.get("<xmlattr>.curveDescripter", "");
std::string x_desc, y_desc;
str_split(curveDesc, ';', x_desc, y_desc);
blk->meta["curveDescriptor"] = curveDesc;
blk->meta["state"] = j->second.get("<xmlattr>.state", "");
string detector = j->second.get("<xmlattr>.detector", "");
blk->meta["detector"] = detector;
blk->meta["startDate"] = j->second.get("<xmlattr>.startDate", "");
blk->meta["offset"] = j->second.get("<xmlattr>.offset", "");
VecColumn *x_col = new VecColumn;
x_col->set_name(x_desc);
std::istringstream curve_ss(j->second.data());
if (j->second.get("<xmlattr>.detector", "") != "Spectrometer") {
VecColumn *y_col = new VecColumn;
y_col->set_name(y_desc);

// read data between <Curve> ... </Curve>
std::string token;
while (std::getline(curve_ss, token, ';')) {
size_t pos = token.find(',');
if (pos != std::string::npos) {
x_col->add_val(my_strtod(token.substr(0, pos)));
y_col->add_val(my_strtod(token.substr(pos+1)));
}
}

blk->add_column(x_axis_col);

//read counts
std::string intens = j->second.data();
std::istringstream data_ss(intens);
std::string data_split, data_split_2, data_split_3;

//set counter 0 for decision if x- or y-axis
int it_data = 0;

while(std::getline(data_ss, data_split, ';')) {

std::istringstream data_ss2(data_split);

while(std::getline(data_ss2, data_split_2, ',')) {

VecColumn *y_col_intens = new VecColumn;

it_data++;
if(it_data %2 == 1){
// times.push_back(data_split_2);
}else {

// remove [ and ] from string
int last_br = data_split_2.find("]");
data_split_2.erase(last_br,1);
data_split_2.erase(0,1);

std::istringstream data_ss3(data_split_2);

while(std::getline(data_ss3, data_split_3, '|')) {

y_col_intens -> add_values_from_str(data_split_3);

}

y_col_intens-> set_name("cts [1/ch]");

blk->add_column(y_col_intens);
} // end else
} // end while 2
} // end while 1

//get curveDescripter
string curveDescriptor = j -> second.get("<xmlattr>.curveDescripter","");
std::vector<std::string> curve_descriptor_split;
boost::split(curve_descriptor_split, curveDescriptor, boost::is_any_of(";"));

//set names of columns
x_axis_col-> set_name(curve_descriptor_split[1]);

string recordType = i -> second.get("<xmlattr>.recordType","");
string state = j -> second.get("<xmlattr>.state","");
string parentID = j-> second.get("<xmlattr>.state","");
string startDate = j -> second.get("<xmlattr>.startDate","");
string curveType = j -> second.get("<xmlattr>.curveType","");
string detector = j -> second.get("<xmlattr>.detector","");
string offset= j -> second.get("<xmlattr>.offset","");
string duration = j -> second.get("<xmlattr>.duration","");
string calibration = j -> second.get("<xmlattr>.calibration","");
string cameraType = j -> second.get("<xmlattr>.cameraType","");
string integrationTime = j -> second.get("<xmlattr>.integrationTime","");
string channelTime = j -> second.get("<xmlattr>.channelTime","");
string CCD_temperature = j -> second.get("<xmlattr>.CCD_temperature","");

//add meta data
blk->meta["state"] = state;
blk->meta["parentID"] = parentID;
blk->meta["startDate"] = startDate;
blk->meta["curveTyp"] = curveType;
blk->meta["detector"] = detector;
blk->meta["offset"] = offset;
blk->meta["duration"] = duration;
blk->meta["calibration"] = calibration;
blk->meta["cameraType"] = cameraType;
blk->meta["integrationTime"] = integrationTime;
blk->meta["channelTime"] = channelTime;
blk->meta["CCD_temperature"] = CCD_temperature;
blk->meta["curveDescriptor"] = curveDescriptor;

//set name of block
ostringstream convert_AQ, convert_measurement_nr;
convert_AQ << AQ_nr;
convert_measurement_nr << measurement_nr;

blk->set_name("AQ: " + convert_AQ.str() + ", Meas.: " +
convert_measurement_nr.str() + ", Type: " + recordType + " (" + detector +")");
blk->meta["stimulator"] = j->second.get("<xmlattr>.stimulator", "");

blk->add_column(x_col);
blk->add_column(y_col);
} else { // detector="Spectrometer"
// read wavelength from attribute "wavelengthTable"
std::string wavelengths = j->second.get("<xmlattr>.wavelengthTable", "");
x_col->add_values_from_str(wavelengths, ';');
blk->add_column(x_col);

// read data between <Curve> ... </Curve>
std::string token;
while (std::getline(curve_ss, token, ';')) {
size_t pos = token.find(',');
size_t open_br = token.find('[', pos);
size_t close_br = token.find(']', open_br);
if (close_br != std::string::npos) {
VecColumn *y_col = new VecColumn;
y_col->set_name(str_trim(token.substr(0, pos)));
// read [y1|y2|...yn]
std::string ystr(token, open_br+1, close_br-open_br-1);
y_col->add_values_from_str(ystr, '|');
blk->add_column(y_col);
}
}

//add meta data
blk->meta["detector"] = detector;
blk->meta["state"] = state;
blk->meta["parentID"] = parentID;
blk->meta["startDate"] = startDate;

//finally: add block
add_block(blk);

} // end if Spectrometer
} // end if detector != ""
} // end if measured
} // end loop curves
} // end loop measurements
} // end loop aliquots


blk->meta["startDate"] = j->second.get("<xmlattr>.startDate", "");
blk->meta["duration"] = j->second.get("<xmlattr>.duration", "");
blk->meta["calibration"] = j->second.get("<xmlattr>.calibration", "");
blk->meta["cameraType"] = j->second.get("<xmlattr>.cameraType", "");
blk->meta["integrationTime"] = j->second.get("<xmlattr>.integrationTime", "");
blk->meta["channelTime"] = j->second.get("<xmlattr>.channelTime", "");
blk->meta["CCD_temperature"] = j->second.get("<xmlattr>.CCD_temperature", "");
}
ostringstream name;
name << "AQ: " << AQ_nr << ", Meas.: " << measurement_nr
<< ", Type: " << recordType << " (" << detector << ')';
blk->set_name(name.str());
add_block(blk);
} // end loop curves
} // end loop measurements
}
} // end load_data

}// namespace xylib

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