OpenMS

Functions  
double  optimalLinearFixedPoint (const double *data, size_t dataSize) 
double  optimalLinearFixedPointMass (const double *data, size_t dataSize, double mass_acc) 
size_t  encodeLinear (const double *data, const size_t dataSize, unsigned char *result, double fixedPoint) 
void  encodeLinear (const std::vector< double > &data, std::vector< unsigned char > &result, double fixedPoint) 
size_t  decodeLinear (const unsigned char *data, const size_t dataSize, double *result) 
void  decodeLinear (const std::vector< unsigned char > &data, std::vector< double > &result) 
size_t  encodeSafe (const double *data, const size_t dataSize, unsigned char *result) 
size_t  decodeSafe (const unsigned char *data, const size_t dataSize, double *result) 
size_t  encodePic (const double *data, const size_t dataSize, unsigned char *result) 
void  encodePic (const std::vector< double > &data, std::vector< unsigned char > &result) 
size_t  decodePic (const unsigned char *data, const size_t dataSize, double *result) 
void  decodePic (const std::vector< unsigned char > &data, std::vector< double > &result) 
double  optimalSlofFixedPoint (const double *data, size_t dataSize) 
size_t  encodeSlof (const double *data, const size_t dataSize, unsigned char *result, double fixedPoint) 
void  encodeSlof (const std::vector< double > &data, std::vector< unsigned char > &result, double fixedPoint) 
size_t  decodeSlof (const unsigned char *data, const size_t dataSize, double *result) 
void  decodeSlof (const std::vector< unsigned char > &data, std::vector< double > &result) 
void ms::numpress::MSNumpress::decodeLinear  (  const std::vector< unsigned char > &  data, 
std::vector< double > &  result  
) 
Calls lower level decodeLinear while handling vector sizes appropriately
Note that this method may throw a const char* if it deems the input data to be corrupt, i.e.. that the last encoded int does not use the last byte in the data. In addition the last encoded int need to use either the last halfbyte, or the second last followed by a 0x0 halfbyte.
data  vector of bytes to be decoded 
result  vector of resulting double (will be resized to the number of doubles) 
size_t ms::numpress::MSNumpress::decodeLinear  (  const unsigned char *  data, 
const size_t  dataSize,  
double *  result  
) 
Decodes data encoded by encodeLinear.
result vector guaranteed to be shorter or equal to (data  8) * 2
Note that this method may throw a const char* if it deems the input data to be corrupt, i.e. that the last encoded int does not use the last byte in the data. In addition the last encoded int need to use either the last halfbyte, or the second last followed by a 0x0 halfbyte.
data  pointer to array of bytes to be decoded (need memorycont. repr.) 
dataSize  number of bytes from *data to decode 
result  pointer to were resulting doubles should be stored 
return  the number of decoded doubles, or 1 if dataSize < 4 or 4 < dataSize < 8 
void ms::numpress::MSNumpress::decodePic  (  const std::vector< unsigned char > &  data, 
std::vector< double > &  result  
) 
Calls lower level decodePic while handling vector sizes appropriately
Note that this method may throw a const char* if it deems the input data to be corrupt, i.e. that the last encoded int does not use the last byte in the data. In addition the last encoded int need to use either the last halfbyte, or the second last followed by a 0x0 halfbyte.
data  vector of bytes to be decoded 
size_t ms::numpress::MSNumpress::decodePic  (  const unsigned char *  data, 
const size_t  dataSize,  
double *  result  
) 
Decodes data encoded by encodePic
result vector guaranteed to be shorter of equal to data * 2
Note that this method may throw a const char* if it deems the input data to be corrupt, i.e. that the last encoded int does not use the last byte in the data. In addition the last encoded int need to use either the last halfbyte, or the second last followed by a 0x0 halfbyte.
data  pointer to array of bytes to be decoded (need memorycont. repr.) 
dataSize  number of bytes from *data to decode 
result  pointer to were resulting doubles should be stored 
size_t ms::numpress::MSNumpress::decodeSafe  (  const unsigned char *  data, 
const size_t  dataSize,  
double *  result  
) 
Decodes data encoded by encodeSafe.
result vector is the same size as the input data.
Might throw const char* is something goes wrong during decoding.
data  pointer to array of bytes to be decoded (need memorycont. repr.) 
dataSize  number of bytes from *data to decode 
result  pointer to were resulting doubles should be stored 
void ms::numpress::MSNumpress::decodeSlof  (  const std::vector< unsigned char > &  data, 
std::vector< double > &  result  
) 
Calls lower level decodeSlof while handling vector sizes appropriately
Note that this method may throw a const char* if it deems the input data to be corrupt.
data  vector of bytes to be decoded 
result  vector of resulting double (will be resized to the number of doubles) 
size_t ms::numpress::MSNumpress::decodeSlof  (  const unsigned char *  data, 
const size_t  dataSize,  
double *  result  
) 
Decodes data encoded by encodeSlof
The return will include exactly (data  8) / 2 doubles.
Note that this method may throw a const char* if it deems the input data to be corrupt.
data  pointer to array of bytes to be decoded (need memorycont. repr.) 
dataSize  number of bytes from *data to decode 
result  pointer to were resulting doubles should be stored 
size_t ms::numpress::MSNumpress::encodeLinear  (  const double *  data, 
const size_t  dataSize,  
unsigned char *  result,  
double  fixedPoint  
) 
Encodes the doubles in data by first using a
The resulting binary is maximally 8 + dataSize * 5 bytes, but much less if the data is reasonably smooth on the first order.
This encoding is suitable for typical m/z or retention time binary arrays. On a test set, the encoding was empirically show to be accurate to at least 0.002 ppm.
data  pointer to array of double to be encoded (need memorycont. repr.) 
dataSize  number of doubles from *data to encode 
result  pointer to where resulting bytes should be stored 
fixedPoint  the scaling factor used for getting the fixed point repr. This is stored in the binary and automatically extracted on decoding. 
void ms::numpress::MSNumpress::encodeLinear  (  const std::vector< double > &  data, 
std::vector< unsigned char > &  result,  
double  fixedPoint  
) 
Calls lower level encodeLinear while handling vector sizes appropriately
data  vector of doubles to be encoded 
result  vector of resulting bytes (will be resized to the number of bytes) 
size_t ms::numpress::MSNumpress::encodePic  (  const double *  data, 
const size_t  dataSize,  
unsigned char *  result  
) 
Encodes ion counts by simply rounding to the nearest 4 byte integer, and compressing each integer with encodeInt.
The handleable range is therefore 0 > 4294967294. The resulting binary is maximally dataSize * 5 bytes, but much less if the data is close to 0 on average.
data  pointer to array of double to be encoded (need memorycont. repr.) 
dataSize  number of doubles from *data to encode 
result  pointer to where resulting bytes should be stored 
void ms::numpress::MSNumpress::encodePic  (  const std::vector< double > &  data, 
std::vector< unsigned char > &  result  
) 
Calls lower level encodePic while handling vector sizes appropriately
data  vector of doubles to be encoded 
result  vector of resulting bytes (will be resized to the number of bytes) 
size_t ms::numpress::MSNumpress::encodeSafe  (  const double *  data, 
const size_t  dataSize,  
unsigned char *  result  
) 
Encodes the doubles in data by storing the residuals from a linear prediction after first two values.
The resulting binary is the same size as the input data.
This encoding is suitable for typical m/z or retention time binary arrays, and is intended to be used before zlib compression to improve compression.
data  pointer to array of doubles to be encoded (need memorycont. repr.) 
dataSize  number of doubles from *data to encode 
result  pointer to were resulting bytes should be stored 
size_t ms::numpress::MSNumpress::encodeSlof  (  const double *  data, 
const size_t  dataSize,  
unsigned char *  result,  
double  fixedPoint  
) 
Encodes ion counts by taking the natural logarithm, and storing a fixed point representation of this. This is calculated as
unsigned short fp = log(d + 1) * fixedPoint + 0.5
the result vector is exactly data * 2 + 8 bytes long
data  pointer to array of double to be encoded (need memorycont. repr.) 
dataSize  number of doubles from *data to encode 
result  pointer to were resulting bytes should be stored 
void ms::numpress::MSNumpress::encodeSlof  (  const std::vector< double > &  data, 
std::vector< unsigned char > &  result,  
double  fixedPoint  
) 
Calls lower level encodeSlof while handling vector sizes appropriately
data  vector of doubles to be encoded 
double ms::numpress::MSNumpress::optimalLinearFixedPoint  (  const double *  data, 
size_t  dataSize  
) 
Compute the maximal linear fixed point that prevents integer overflow.
data  pointer to array of double to be encoded (need memorycont. repr.) 
dataSize  number of doubles from *data to encode 
double ms::numpress::MSNumpress::optimalLinearFixedPointMass  (  const double *  data, 
size_t  dataSize,  
double  mass_acc  
) 
Compute the optimal linear fixed point with a desired m/z accuracy.
data  pointer to array of double to be encoded (need memorycont. repr.) 
dataSize  number of doubles from *data to encode 
mass_acc  desired m/z accuracy in Th 
double ms::numpress::MSNumpress::optimalSlofFixedPoint  (  const double *  data, 
size_t  dataSize  
) 