Data structures and methods to read/write experimental data. More...

#include "us_dataIO.h"

Classes
class	BeckmanRawScan
	Beckman Raw data scan. More...

class	EditedData
	The CCW data after edits are applied. More...

class	EditedPoint
	Changes made to a scan value. More...

class	EditValues
	Entries for edits of a scan. More...

class	NewEditedData
	The CCW data after edits are applied. More...

class	Parameters
	A private convenience class. More...

class	RawData
	All data associated with a cell / channel / wavelength (CCW) More...

class	Scan
	Single scan parameter and readings. More...

class	SpeedData
	Additional data for each triplet, if equilibrium data. More...

Public Types
enum	ioError { OK, CANTOPEN, BADCRC, NOT_USDATA, BADTYPE, BADXML, NODATA, NO_GUID_MATCH, BAD_VERSION }
	Values that are returned for various errors when managing scan data. More...

Static Public Member Functions
static bool	readLegacyFile (const QString &, BeckmanRawScan &)

static int	writeRawData (const QString &, RawData &)

static int	readRawData (const QString &, RawData &)

static int	readEdits (const QString &, EditValues &)

static QString	errorString (int)

static int	index (const QVector< double > &, double)

static int	index (US_DataIO::RawData *, double)

static int	index (US_DataIO::EditedData *, double)

static int	loadData (const QString &, const QString &, QVector< EditedData > &, QVector< RawData > &)

static int	loadData (const QString &, const QString &, QVector< EditedData > &)

static int	loadData (const QString &, const QString &, EditedData &)

static void	adjust_interference (RawData &, const EditValues &)

static void	calc_integral (RawData &, const EditValues &)

static bool	spike_check (const Scan &, const QVector< double > &, int, int, int, double *)

Static Public Attributes
static const uint	format_version = 5

Static Private Member Functions
static void	writeScan (QDataStream &, const Scan &, quint32 &, const Parameters &)

static void	write (QDataStream &, const char *, int, quint32 &)

static void	read (QDataStream &, char *, int, quint32 &)

static void	ident (QXmlStreamReader &, EditValues &)

static void	run (QXmlStreamReader &, EditValues &)

static void	all_lambdas (QXmlStreamReader &, EditValues &)

static void	excludes (QXmlStreamReader &, EditValues &)

static void	params (QXmlStreamReader &, EditValues &)

static void	operations (QXmlStreamReader &, EditValues &)

static void	do_edits (QXmlStreamReader &, EditValues &)

static void	copyRange (double, double, const Scan &, Scan &, const QVector< double > &)

static void	copyxRange (double, double, const QVector< double > &, QVector< double > &)

static QList< double >	calc_residuals (int, const QVector< Scan > &)

Detailed Description

Data structures and methods to read/write experimental data.

The US_DataIO class provides data structures and static methods to read and write experimental data.

For memory efficiency, there is only a single vector of radius values that applies to all the scans. So for instance, if you have an instance of RawData or EditedData like this:

EditedData* data;

you could refer to an individual scan reading value like this:

data->scanData[ scanIndex ].rvalues[ readingIndex ]

Definition at line 24 of file us_dataIO.h.

Member Enumeration Documentation

enum US_DataIO::ioError

Values that are returned for various errors when managing scan data.

Enumerator
OK
CANTOPEN
BADCRC
NOT_USDATA
BADTYPE
BADXML
NODATA
NO_GUID_MATCH
BAD_VERSION

Definition at line 245 of file us_dataIO.h.

Member Function Documentation

void US_DataIO::adjust_interference	(	RawData &	data,
		const EditValues &	ev
	)

static

Adjust interference data by aligning air gaps at zero fringes

Parameters

data	A reference to the RawData structure to be adjusted
ev	The EditValues used for the adjustment. Only airGapLeft, airGapRight, and includes are needed.

Definition at line 1202 of file us_dataIO.cpp.

void US_DataIO::all_lambdas	(	QXmlStreamReader &	xml,
		EditValues &	parameters
	)

staticprivate

Definition at line 831 of file us_dataIO.cpp.

void US_DataIO::calc_integral	(	RawData &	data,
		const EditValues &	ee
	)

static

Align integral fringe shifts within the valid data range

Parameters

data	A reference to the RawData structure to be adjusted
ee	The EditValues used for the adjustment. Only rangeLeft, rangeRight, and gapTolerance are needed.

Definition at line 1251 of file us_dataIO.cpp.

QList< double > US_DataIO::calc_residuals	(	int	order,
		const QVector< Scan > &	sl
	)

staticprivate

Definition at line 1553 of file us_dataIO.cpp.

void US_DataIO::copyRange	(	double	left,
		double	right,
		const Scan &	orig,
		Scan &	dest,
		const QVector< double > &	origx
	)

staticprivate

Definition at line 1362 of file us_dataIO.cpp.

void US_DataIO::copyxRange	(	double	left,
		double	right,
		const QVector< double > &	origx,
		QVector< double > &	destx
	)

staticprivate

Definition at line 1416 of file us_dataIO.cpp.

void US_DataIO::do_edits	(	QXmlStreamReader &	xml,
		EditValues &	parameters
	)

staticprivate

Definition at line 971 of file us_dataIO.cpp.

QString US_DataIO::errorString ( int code )

static

A string describing the last read or write error

Parameters

code	The error code to be described

Definition at line 1651 of file us_dataIO.cpp.

void US_DataIO::excludes	(	QXmlStreamReader &	xml,
		EditValues &	parameters
	)

staticprivate

Definition at line 955 of file us_dataIO.cpp.

void US_DataIO::ident	(	QXmlStreamReader &	xml,
		EditValues &	parameters
	)

staticprivate

Definition at line 773 of file us_dataIO.cpp.

int US_DataIO::index	(	const QVector< double > &	xvals,
		double	xvalue
	)

static

Determine the index of a radius in a vector of radii

Parameters

xvals	A vector of data radius information
xvalue	The radius where the index is needed

Definition at line 1620 of file us_dataIO.cpp.

int US_DataIO::index	(	US_DataIO::RawData *	rdata,
		double	xvalue
	)

static

Determine the index of a radius in a RawData set

Parameters

rdata	A pointer to the RawData set to examine
xvalue	The radius where the index is needed

Definition at line 1608 of file us_dataIO.cpp.

int US_DataIO::index	(	US_DataIO::EditedData *	edata,
		double	xvalue
	)

static

Determine the index of a radius in an EditedData set

Parameters

edata	A pointer to the EditedData set to examine
xvalue	The radius where the index is needed

Definition at line 1614 of file us_dataIO.cpp.

int US_DataIO::loadData	(	const QString &	directory,
		const QString &	editFilename,
		QVector< EditedData > &	data,
		QVector< RawData > &	raw
	)

static

Load edited data into a data structure. This is the method most analysis programs will call to read data into memory. It uses the functions readRawData and readEdits.

Parameters

directory	The directory of the auc files
editFilename	The the file with the edited parameters
data	The location where the edited data is placed
raw	The location where the raw data is placed

Definition at line 1017 of file us_dataIO.cpp.

int US_DataIO::loadData	(	const QString &	directory,
		const QString &	editFilename,
		QVector< EditedData > &	data
	)

static

This is an overloaded method to read data into memory. It uses the functions readRawData and readEdits.

Parameters

directory	The directory of the auc files
editFilename	The the file with the edited parameters
data	The location where the edited data is placed

Definition at line 992 of file us_dataIO.cpp.

int US_DataIO::loadData	(	const QString &	directory,
		const QString &	editFilename,
		EditedData &	data
	)

static

This is an overloaded method to read data into memory. It uses the functions readRawData and readEdits.

Parameters

directory	The directory of the auc files
editFilename	The the file with the edited parameters
data	The location where the edited data is placed

Definition at line 1001 of file us_dataIO.cpp.

void US_DataIO::operations	(	QXmlStreamReader &	xml,
		EditValues &	parameters
	)

staticprivate

Definition at line 930 of file us_dataIO.cpp.

void US_DataIO::params	(	QXmlStreamReader &	xml,
		EditValues &	parameters
	)

staticprivate

Definition at line 847 of file us_dataIO.cpp.

void US_DataIO::read	(	QDataStream &	ds,
		char *	cc,
		int	len,
		quint32 &	crc
	)

staticprivate

Definition at line 732 of file us_dataIO.cpp.

int US_DataIO::readEdits	(	const QString &	filename,
		EditValues &	parameters
	)

static

Read a set of edit parameters in xml format

Parameters

filename	The filename to be read
parameters	A reference to the data structure for the read data

Definition at line 738 of file us_dataIO.cpp.

bool US_DataIO::readLegacyFile	(	const QString &	file,
		BeckmanRawScan &	data
	)

static

Read a set of legacy data in raw teckman data set format

Parameters

file	The filename to be read
data	A reference to the data structure location for read data

Definition at line 193 of file us_dataIO.cpp.

int US_DataIO::readRawData	(	const QString &	file,
		RawData &	data
	)

static

Read a set of data in the US3 binary format

Parameters

file	The filename to be read
data	A reference to the data structure for the read data

Definition at line 500 of file us_dataIO.cpp.

void US_DataIO::run	(	QXmlStreamReader &	xml,
		EditValues &	parameters
	)

staticprivate

Definition at line 801 of file us_dataIO.cpp.

bool US_DataIO::spike_check	(	const Scan &	sc,
		const QVector< double > &	xvalues,
		int	point,
		int	start,
		int	end,
		double *	value
	)

static

Check a scan point to see if it is a spike relative to the non-interpolated points around it

Parameters

sc	The scan to check
xvalues	The vector of radius values associated with the scan
point	The inde of the point to check
start	The beginning of the valid scan range
end	The end of the valid scan range
value	The value of the interpolated point if a spike is detected

Returns: A flag indication if the point is a spike

Definition at line 1427 of file us_dataIO.cpp.

void US_DataIO::write	(	QDataStream &	ds,
		const char *	c,
		int	len,
		quint32 &	crc
	)

staticprivate

Definition at line 494 of file us_dataIO.cpp.

int US_DataIO::writeRawData	(	const QString &	file,
		RawData &	data
	)

static

Write a set of data to a file in the US3 binary format

Parameters

file	The filename to be read
data	A reference to the data structure of the data to be written

Definition at line 260 of file us_dataIO.cpp.

void US_DataIO::writeScan	(	QDataStream &	ds,
		const Scan &	data,
		quint32 &	crc,
		const Parameters &	pp
	)

staticprivate

Definition at line 414 of file us_dataIO.cpp.

Member Data Documentation

const uint US_DataIO::format_version = 5

static

A constant value that identifies the format of the auc raw data. Internal programs use this value to determine if the format of the file is known.

Definition at line 31 of file us_dataIO.h.

The documentation for this class was generated from the following files:

Classes

Public Types

Static Public Member Functions

Static Public Attributes

Static Private Member Functions

Detailed Description

Member Enumeration Documentation

Member Function Documentation

Member Data Documentation