void autotrim(boost::shared_ptr<pcl::PointCloud<PointT>> &cloud, double &clip_N, double &clip_S, double &clip_E, double &clip_W, double tolerance) {
struct bound_box bbox;
getMinMax(*cloud, bbox);
double resolution = 0.003;
int length_x = (int)((bbox.E - bbox.W) / resolution + 0.5);
int length_y = (int)((bbox.N - bbox.S) / resolution + 0.5);
std::vector<int> x_array(length_x, 0);
std::vector<int> y_array(length_y, 0);
unsigned int idx;
for(typename pcl::PointCloud<PointT>::iterator it = cloud->begin(); it!= cloud->end(); it++){
idx = int((it->x - bbox.W) / resolution);
if (idx < x_array.size())
x_array[idx] += 1;
idx = int((it->y - bbox.S) / resolution);
if (idx < y_array.size())
y_array[idx] += 1;
}
int median_x = median(x_array);
int median_y = median(y_array);
clip_N = 0;
clip_S = 0;
clip_E = 0;
clip_W = 0;
for (int i = 0; i < x_array.size(); i++) {
if (x_array[i] < tolerance * median_x) {
clip_W = (i + 1) * resolution;
}
else
break;
}
for (int i = x_array.size() - 1; i >= 0; i--) {
if (x_array[i] < tolerance * median_x) {
clip_E = (x_array.size() - i) * resolution;
}
else
break;
}
for (int i = 0; i < y_array.size(); i++) {
if (y_array[i] < tolerance * median_y) {
clip_S = (i + 1) * resolution;
}
else
break;
}
for (int i = y_array.size() - 1; i >= 0; i--) {
if (y_array[i] < tolerance * median_y) {
clip_N = (y_array.size() - i) * resolution;
}
else
break;
}
//std::cout << clip_N << " " << clip_S << " " << clip_E << " " << clip_W << std::endl;
}
OpenMS::Interfaces::SpectrumPtr MzMLSpectrumDecoder::decodeBinaryData(std::vector<BinaryData>& data_)
{
Internal::MzMLHandlerHelper::decodeBase64Arrays(data_);
OpenMS::Interfaces::SpectrumPtr sptr(new OpenMS::Interfaces::Spectrum);
//look up the precision and the index of the intensity and m/z array
bool x_precision_64 = true;
bool int_precision_64 = true;
SignedSize x_index = -1;
SignedSize int_index = -1;
Internal::MzMLHandlerHelper::computeDataProperties_(data_, x_precision_64, x_index, "m/z array");
Internal::MzMLHandlerHelper::computeDataProperties_(data_, int_precision_64, int_index, "intensity array");
//Abort if no m/z or intensity array is present
if (int_index == -1 || x_index == -1)
{
// Warning ...
return sptr;
}
// Error if intensity or m/z is encoded as int32|64 - they should be float32|64!
if ((data_[x_index].ints_32.size() > 0) || (data_[x_index].ints_64.size() > 0))
{
//fatalError(LOAD, "Encoding m/z array as integer is not allowed!");
}
if ((data_[int_index].ints_32.size() > 0) || (data_[int_index].ints_64.size() > 0))
{
//fatalError(LOAD, "Encoding intensity array as integer is not allowed!");
}
// Warn if the decoded data has a different size than the defaultArrayLength
Size mz_size = x_precision_64 ? data_[x_index].floats_64.size() : data_[x_index].floats_32.size();
Size int_size = int_precision_64 ? data_[int_index].floats_64.size() : data_[int_index].floats_32.size();
// Check if int-size and mz-size are equal
if (mz_size != int_size)
{
std::cout << "Warning, intensity and m/z array length are unequal" << std::endl;
return sptr;
}
Size default_array_length_ = mz_size;
// maybe some checks here about internal consistency e.g. with defaultArrayLength ...
//create meta data arrays and reserve enough space for the content
if (data_.size() > 2)
{
// --> TODO the other arrays ... create and resize those ...
}
// Copy meta data from m/z and intensity binary
// We don't have this as a separate location => store it in spectrum
// --> maybe TODO
OpenMS::Interfaces::BinaryDataArrayPtr intensity_array(new OpenMS::Interfaces::BinaryDataArray);
OpenMS::Interfaces::BinaryDataArrayPtr x_array(new OpenMS::Interfaces::BinaryDataArray);
for (Size n = 0; n < default_array_length_; n++)
{
DoubleReal xcoord = x_precision_64 ? data_[x_index].floats_64[n] : data_[x_index].floats_32[n];
DoubleReal intensity = int_precision_64 ? data_[int_index].floats_64[n] : data_[int_index].floats_32[n];
x_array->data.push_back(xcoord);
intensity_array->data.push_back(intensity);
// TODO the other arrays
}
sptr->setMZArray(x_array);
sptr->setIntensityArray(intensity_array);
return sptr;
}
