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

data	vector of bytes to be decoded
result	vector 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

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

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

data	vector of bytes to be decoded

Returns

vector 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

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

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

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

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

data	vector of bytes to be decoded
result	vector 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

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

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

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.

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

data	vector of doubles to be encoded
result	vector of resulting bytes (will be resized to the number of bytes)

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

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

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

data	vector of doubles to be encoded
result	vector 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

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

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

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

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

data	vector of doubles to be encoded

Returns

vector of resulting bytes (will be resized to the number of bytes)

optimalLinearFixedPoint()

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

Compute the maximal linear fixed point that prevents integer overflow.

Parameters

data	pointer to array of double to be encoded (need memorycont. repr.)
dataSize	number 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

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

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
	)