OpenMS
ms::numpress::MSNumpress Namespace Reference

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)
 

Function Documentation

◆ decodeLinear() [1/2]

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.

Parameters
datavector of bytes to be decoded
resultvector of resulting double (will be resized to the number of doubles)

◆ decodeLinear() [2/2]

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.

Parameters
datapointer to array of bytes to be decoded (need memorycont. repr.)
dataSizenumber of bytes from *data to decode
resultpointer to were resulting doubles should be stored
Returns
the number of decoded doubles, or -1 if dataSize < 4 or 4 < dataSize < 8

◆ decodePic() [1/2]

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.

Parameters
datavector of bytes to be decoded
resultvector of resulting double (will be resized to the number of doubles)

◆ decodePic() [2/2]

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.

Parameters
datapointer to array of bytes to be decoded (need memorycont. repr.)
dataSizenumber of bytes from *data to decode
resultpointer to were resulting doubles should be stored
Returns
the number of decoded doubles

◆ decodeSafe()

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.

Parameters
datapointer to array of bytes to be decoded (need memorycont. repr.)
dataSizenumber of bytes from *data to decode
resultpointer to were resulting doubles should be stored
Returns
the number of decoded bytes

◆ decodeSlof() [1/2]

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.

Parameters
datavector of bytes to be decoded
resultvector of resulting double (will be resized to the number of doubles)

◆ decodeSlof() [2/2]

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.

Parameters
datapointer to array of bytes to be decoded (need memorycont. repr.)
dataSizenumber of bytes from *data to decode
resultpointer to were resulting doubles should be stored
Returns
the number of decoded doubles

◆ encodeLinear() [1/2]

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

  • lossy conversion to a 4 byte 5 decimal fixed point representation
  • storing the residuals from a linear prediction after first two values
  • encoding by encodeInt (see above)

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.

Parameters
datapointer to array of double to be encoded (need memorycont. repr.)
dataSizenumber of doubles from *data to encode
resultpointer to where resulting bytes should be stored
fixedPointthe scaling factor used for getting the fixed point repr. This is stored in the binary and automatically extracted on decoding.
Returns
the number of encoded bytes

◆ encodeLinear() [2/2]

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

Parameters
datavector of doubles to be encoded
resultvector of resulting bytes (will be resized to the number of bytes)
fixedPointthe scaling factor used for getting the fixed point repr. This is stored in the binary and automatically extracted on decoding.

◆ encodePic() [1/2]

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.

Parameters
datapointer to array of double to be encoded (need memorycont. repr.)
dataSizenumber of doubles from *data to encode
resultpointer to where resulting bytes should be stored
Returns
the number of encoded bytes

◆ encodePic() [2/2]

void ms::numpress::MSNumpress::encodePic ( const std::vector< double > &  data,
std::vector< unsigned char > &  result 
)

Calls lower level encodePic while handling vector sizes appropriately

Parameters
datavector of doubles to be encoded
resultvector of resulting bytes (will be resized to the number of bytes)

◆ encodeSafe()

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.

Parameters
datapointer to array of doubles to be encoded (need memorycont. repr.)
dataSizenumber of doubles from *data to encode
resultpointer to were resulting bytes should be stored

◆ encodeSlof() [1/2]

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

Parameters
datapointer to array of double to be encoded (need memorycont. repr.)
dataSizenumber of doubles from *data to encode
resultpointer to were resulting bytes should be stored
fixedPointthe scaling factor used for getting the fixed point repr. This is stored in the binary and automatically extracted on decoding.
Returns
the number of encoded bytes

◆ encodeSlof() [2/2]

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

Parameters
datavector of doubles to be encoded
resultvector of resulting bytes (will be resized to the number of bytes)
fixedPointthe scaling factor used for getting the fixed point repr. This is stored in the binary and automatically extracted on decoding.

◆ optimalLinearFixedPoint()

double ms::numpress::MSNumpress::optimalLinearFixedPoint ( const double *  data,
size_t  dataSize 
)

Compute the maximal linear fixed point that prevents integer overflow.

Parameters
datapointer to array of double to be encoded (need memorycont. repr.)
dataSizenumber of doubles from *data to encode
Returns
the linear fixed point safe to use

◆ optimalLinearFixedPointMass()

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.

Note
If the desired accuracy cannot be reached without overflowing 64 bit integers, then a negative value is returned. You need to check for this and in that case abandon numpress or use optimalLinearFixedPoint which returns the largest safe value.
Parameters
datapointer to array of double to be encoded (need memorycont. repr.)
dataSizenumber of doubles from *data to encode
mass_accdesired m/z accuracy in Th
Returns
the linear fixed point that satisfies the accuracy requirement (or -1 in case of failure).

◆ optimalSlofFixedPoint()

double ms::numpress::MSNumpress::optimalSlofFixedPoint ( const double *  data,
size_t  dataSize 
)