Create a radial average of q values from a raw detector image. More...

#include <image_manipulation.h>

Inheritance diagram for cass::pp90:

Collaboration diagram for cass::pp90:

Classes
struct	temp_t
	define the table row of a single output More...

Public Member Functions
	pp90 (const name_t &)
	constructor More...

virtual void	process (const CASSEvent &evt, result_t &)
	process event More...

virtual void	loadSettings (size_t unused)
	load the settings of this pp More...

Public Member Functions inherited from cass::Processor
	Processor (const name_t &name)
	constructor More...

virtual	~Processor ()
	virtual destructor More...

virtual void	processEvent (const CASSEvent &event)
	process the event More...

virtual const result_t &	result (const CASSEvent::id_t eventid=0)
	retrieve a result for a given id. More...

virtual void	releaseEvent (const CASSEvent &event)
	tell the list that the result for event can be overwritten More...

result_t::shared_pointer	resultCopy (const uint64_t eventid)
	retrieve histogram for id More...

virtual void	load ()
	load the general settings More...

virtual void	aboutToQuit ()
	function that will be called when the processor is about to be deleted More...

const names_t &	dependencies ()
	Define all processors keys a processor depends on. More...

void	clearDependencies ()
	clear the dependenies More...

void	clearHistograms ()
	clear the histograms More...

virtual void	processCommand (std::string command)
	process command in pp More...

const name_t	name () const
	retrieve the name of this processor More...

bool	hide () const
	retrieve the hide flag of this processor More...

const std::string &	comment () const
	retrieve the comment of this processor More...

Protected Types
typedef std::vector< temp_t >	tempArray_t
	define the matrix More...

typedef std::vector< result_t::value_t >	normfactors_t
	define the normalization factors More...

Protected Member Functions
double	wlFromConstant (const CASSEvent::id_t &)
	retrieve the constant wavelength More...

double	wlFromProcessor (const CASSEvent::id_t &id)
	retrieve the wavelength from the processor More...

double	ddFromConstant (const CASSEvent::id_t &)
	retrieve the constant detector distance More...

double	ddFromProcessor (const CASSEvent::id_t &id)
	retrieve the detector distance from the processor More...

temp_t	Q (const double lambda, const double D, const result_t::value_t &pixval, const GeometryInfo::pos_t &pixpos)
	get the bin when the q-value of the pixel is asked More...

temp_t	R (const double lambda, const double D, const result_t::value_t &pixval, const GeometryInfo::pos_t &pixpos)
	get the bin when the resolution value of the pixel is asked More...

temp_t	Rad (const double lambda, const double D, const result_t::value_t &pixval, const GeometryInfo::pos_t &pixpos)
	get the bin when the radius of the pixel is asked More...

Protected Member Functions inherited from cass::Processor
virtual void	createHistList (result_t::shared_pointer result)
	create result list. More...

void	setupGeneral ()
	general setup of the processor More...

bool	setupCondition (bool defaultConditionType=true)
	setup the condition. More...

shared_pointer	setupDependency (const std::string &depVarName, const name_t &name="")
	setup the dependecy. More...

Protected Attributes
shared_pointer	_imagePP
	pp containing 2d histogram More...

bool	_convertCheetahToCASSLayout
	flag whether to convert the positions in the src from cheetah to cass layout More...

std::string	_filename
	filename of the geometry file More...

GeometryInfo::conversion_t	_pixPositions_m
	the pixel positions More...

double	_wavelength
	the wavelength in case its fixed More...

shared_pointer	_wavelengthPP
	pp containing wavelength in case its not fixed More...

std::tr1::function< double(const CASSEvent::id_t &)>	_getWavelength
	function that gets the wavelength More...

double	_detdist
	the detector distance in case its fixed More...

shared_pointer	_detdistPP
	pp containing detector distance in case its not fixed More...

std::tr1::function< double(const CASSEvent::id_t &)>	_getDetectorDistance
	function that gets the detectordistance More...

double	_np_m
	the size of one pixel in m More...

float	_badPixVal
	value of the bad pixels More...

std::tr1::function< temp_t(const double, const double, const result_t::value_t &, const GeometryInfo::pos_t &)>	_getBin
	function to map the pixel to histogram bin, value and fill flag More...

result_t::axe_t	_axis
	the axis of the result More...

Protected Attributes inherited from cass::Processor
const name_t	_name
	the processors name More...

bool	_hide
	flag to tell whether this pp should be hidden in the dropdown list More...

std::string	_comment
	optional comment that one can add to a processor. More...

CachedList	_resultList
	the list of results More...

names_t	_dependencies
	the list of dependencies More...

shared_pointer	_condition
	pointer to the processor that will contain the condition More...

Additional Inherited Members
Public Types inherited from cass::Processor
typedef std::tr1::shared_ptr< Processor >	shared_pointer
	a shared pointer of this More...

typedef std::string	name_t
	define the name type More...

typedef std::list< name_t >	names_t
	define the list of names More...

typedef CachedList::item_type	result_t
	define the results More...

typedef CachedList::item_sp	resultsp_t
	define the shared pointer to the result More...

Detailed Description

Create a radial average of q values from a raw detector image.

Available PostProcessors:: "90": Radial average from detector image using geom

calculate the Q value for each Pixel using the geom file.

See also: Processor for a list of all commonly available cass.ini settings.

User definable Parameters:

Processor/%name%/{ImageName}
the processor name that contains the histogram containing the cspad image in cass layout. Default is "".

Processor/%name%/{GeometryFilename}
The geom file to use. Default is "cspad.geom".

Processor/%name%/{ConvertCheetahToCASSLayout}
Set this true if the geom file is for a cheetah layout of the data, but the image in ImageName is the image in CASS layout.

Processor/%name%/{Wavelength_A}
The wavelength in Angstroem. Can also be the name of a PP that contains the Wavelength. Default is 1.

Processor/%name%/{DetectorDistance_m}
The detector distance in m. Can also be the name of a PP that contains the detector distance. Default is 60e-2.

Processor/%name%/{PixelSize_m}
The pixel size in m. Default is 110e-6

Processor/%name%/{XNbrBins|XLow|XUp}
properties of the resulting 1D histogram

Processor/%name%/{BadPixelValue}
value of the bad pixel in the image. Default is 0

Processor/%name%/{Output}
One can choose the type of radial average that one wants to have. Default is "Q". Possible values are:

"Q": the q-averge in the defintion of q that SAXS people are using. See pp90::Q for details.
"Resolution": the radial average in resultion values as defined by the crystallographers. See pp90::R for details.
"Radius": the radial average in radii, where the Pixelsize_m parameter is used to determine the radius. If one wants to have the radius in pixel units, one just has to set the PixelSize_m parameter to 1.

Author: Lutz Foucar

Definition at line 567 of file image_manipulation.h.

Member Typedef Documentation

typedef std::vector<result_t::value_t> cass::pp90::normfactors_t

protected

define the normalization factors

Definition at line 674 of file image_manipulation.h.

typedef std::vector<temp_t> cass::pp90::tempArray_t

protected

define the matrix

Definition at line 593 of file image_manipulation.h.

Constructor & Destructor Documentation

pp90::pp90 ( const name_t & name )

constructor

Definition at line 550 of file image_manipulation.cpp.

References loadSettings().

Member Function Documentation

double cass::pp90::ddFromConstant ( const CASSEvent::id_t & )

inlineprotected

retrieve the constant detector distance

Parameters

id unused

Definition at line 612 of file image_manipulation.h.

References _detdist.

Referenced by loadSettings().

double pp90::ddFromProcessor ( const CASSEvent::id_t & id )

protected

retrieve the detector distance from the processor

Parameters

id	the id of the event to get the detector distance from

Definition at line 691 of file image_manipulation.cpp.

References _detdistPP.

Referenced by loadSettings().

void pp90::loadSettings ( size_t unused )

virtual

load the settings of this pp

Parameters

unused this parameter is not used

setup the method to be used

use fixed value for wavelength if value can be converted to double, otherwise use the wavelength from the processor

use fixed value for detector distance if value can be converted to double, otherwise use the detector distance from the processor

if the method is radius, assign dummy entries (but non-zero) to the wavelength and detector distance

check if the input processors have the correct type

setup the pixel position map

create the output histogram the storage where to put the normfactors

Reimplemented from cass::Processor.

Definition at line 556 of file image_manipulation.cpp.

References _axis, _badPixVal, cass::Processor::_condition, _convertCheetahToCASSLayout, _detdist, _detdistPP, _filename, _getBin, _getDetectorDistance, _getWavelength, _imagePP, _np_m, _pixPositions_m, _wavelength, _wavelengthPP, cass::Log::add(), cass::Result< T >::axis(), QSettings::beginGroup(), cass::Processor::createHistList(), ddFromConstant(), ddFromProcessor(), QString::fromStdString(), cass::GeometryInfo::generateConversionMap(), cass::Log::INFO, cass::ACQIRIS::method, cass::Processor::name(), Q(), R(), Rad(), cass::Processor::result(), cass::set1DHist(), cass::Processor::setupCondition(), cass::Processor::setupDependency(), cass::Processor::setupGeneral(), cass::toString(), QSettings::value(), wlFromConstant(), wlFromProcessor(), and cass::Result< float >::xAxis.

Referenced by pp90().

void pp90::process	(	const CASSEvent &	evt,
		result_t &	result
	)

virtual

process event

Get the input histogram and its memory

get the wavelenth and detector distance and return if they are bad

iterate through the src image and determine the pixels bin in the result only when they are not masked

now put the weights into the correct bins and create the nomralization factors

normalize by the number of fills for each bin

Reimplemented from cass::Processor.

Definition at line 779 of file image_manipulation.cpp.

References _getBin, _getDetectorDistance, _getWavelength, _imagePP, _pixPositions_m, cass::Result< T >::begin(), cass::Result< T >::datasize(), cass::fuzzyIsNull(), cass::CASSEvent::id(), and cass::Result< T >::lock.

pp90::temp_t pp90::Q	(	const double	lambda,
		const double	D,
		const result_t::value_t &	pixval,
		const GeometryInfo::pos_t &	pixpos
	)

protected

get the bin when the q-value of the pixel is asked

the q-value will be calculated using formula

$Q = \frac{4\pi}{\lambda} \sin\left(\frac{1}{2}\arctan\left(\frac{r}{d}\right)\right)$

with $\lambda$ being the wavelength in $\AA$ , $r$ the radius of the pixel and $d$ the detector distance.

Returns: the struct that tell the bin, value, fill combination

Parameters

lambda	the wavelength
D	the detector distance
pixval	the value of the pixel
pixpos	the position of the pixel in m

Definition at line 698 of file image_manipulation.cpp.

References _axis, _badPixVal, cass::histogramming::bin(), cass::pp90::temp_t::bin, cass::pp90::temp_t::fill, cass::fuzzycompare(), cass::pp90::temp_t::weight, cass::GeometryInfo::pos_t::x, and cass::GeometryInfo::pos_t::y.

Referenced by loadSettings(), and R().

pp90::temp_t pp90::R	(	const double	lambda,
		const double	D,
		const result_t::value_t &	pixval,
		const GeometryInfo::pos_t &	pixpos
	)

protected

get the bin when the resolution value of the pixel is asked

the resultion will be calculated as follows

$R = \frac{1}{\frac{2}{\lambda}\sin\left(\frac{1}{2}\arctan\left(\frac{r}{d}\right)\right)}$

with $\lambda$ being the wavelength in $\AA$ , $r$ the radius of the pixel and $d$ the detector distance.

Returns: the struct that tell the bin, value, fill combination

Parameters

lambda	the wavelength
D	the detector distance
pixval	the value of the pixel
pixpos	the position of the pixel in m

Definition at line 722 of file image_manipulation.cpp.

References _axis, _badPixVal, cass::histogramming::bin(), cass::pp90::temp_t::bin, cass::pp90::temp_t::fill, cass::fuzzycompare(), Q(), cass::pp90::temp_t::weight, cass::GeometryInfo::pos_t::x, and cass::GeometryInfo::pos_t::y.

Referenced by loadSettings().

pp90::temp_t pp90::Rad	(	const double	lambda,
		const double	D,
		const result_t::value_t &	pixval,
		const GeometryInfo::pos_t &	pixpos
	)

protected

get the bin when the radius of the pixel is asked

Returns: the struct that tell the bin, value, fill combination

Parameters

lambda	unused
D	unused
pixval	the value of the pixel
pixpos	the position of the pixel in m

Definition at line 748 of file image_manipulation.cpp.

References _axis, _badPixVal, cass::histogramming::bin(), cass::pp90::temp_t::bin, cass::pp90::temp_t::fill, cass::fuzzycompare(), cass::pp90::temp_t::weight, cass::GeometryInfo::pos_t::x, and cass::GeometryInfo::pos_t::y.

Referenced by loadSettings().

double cass::pp90::wlFromConstant ( const CASSEvent::id_t & )

inlineprotected

retrieve the constant wavelength

Parameters

id unused

Definition at line 600 of file image_manipulation.h.

References _wavelength.

Referenced by loadSettings().

double pp90::wlFromProcessor ( const CASSEvent::id_t & id )

protected

retrieve the wavelength from the processor

Parameters

id	the id of the event to get the wavelength from

Definition at line 684 of file image_manipulation.cpp.

References _wavelengthPP.

Referenced by loadSettings().

Member Data Documentation

result_t::axe_t cass::pp90::_axis

protected

the axis of the result

Definition at line 714 of file image_manipulation.h.

Referenced by loadSettings(), Q(), R(), and Rad().

float cass::pp90::_badPixVal

protected

value of the bad pixels

Definition at line 707 of file image_manipulation.h.

Referenced by loadSettings(), Q(), R(), and Rad().

bool cass::pp90::_convertCheetahToCASSLayout

protected

flag whether to convert the positions in the src from cheetah to cass layout

Definition at line 677 of file image_manipulation.h.

Referenced by loadSettings().

double cass::pp90::_detdist

protected

the detector distance in case its fixed

Definition at line 695 of file image_manipulation.h.

Referenced by ddFromConstant(), and loadSettings().

shared_pointer cass::pp90::_detdistPP

protected

pp containing detector distance in case its not fixed

Definition at line 698 of file image_manipulation.h.

Referenced by ddFromProcessor(), and loadSettings().

std::string cass::pp90::_filename

protected

filename of the geometry file

Definition at line 680 of file image_manipulation.h.

Referenced by loadSettings().

std::tr1::function<temp_t(const double,const double,const result_t::value_t&, const GeometryInfo::pos_t&)> cass::pp90::_getBin

protected

function to map the pixel to histogram bin, value and fill flag

Definition at line 711 of file image_manipulation.h.

Referenced by loadSettings(), and process().

std::tr1::function<double(const CASSEvent::id_t&)> cass::pp90::_getDetectorDistance

protected

function that gets the detectordistance

Definition at line 701 of file image_manipulation.h.

Referenced by loadSettings(), and process().

std::tr1::function<double(const CASSEvent::id_t&)> cass::pp90::_getWavelength

protected

function that gets the wavelength

Definition at line 692 of file image_manipulation.h.

Referenced by loadSettings(), and process().

shared_pointer cass::pp90::_imagePP

protected

pp containing 2d histogram

Definition at line 671 of file image_manipulation.h.

Referenced by loadSettings(), and process().

double cass::pp90::_np_m

protected

the size of one pixel in m

Definition at line 704 of file image_manipulation.h.

Referenced by loadSettings().

GeometryInfo::conversion_t cass::pp90::_pixPositions_m

protected

the pixel positions

Definition at line 683 of file image_manipulation.h.

Referenced by loadSettings(), and process().

double cass::pp90::_wavelength

protected

the wavelength in case its fixed

Definition at line 686 of file image_manipulation.h.

Referenced by loadSettings(), and wlFromConstant().

shared_pointer cass::pp90::_wavelengthPP

protected

pp containing wavelength in case its not fixed

Definition at line 689 of file image_manipulation.h.

Referenced by loadSettings(), and wlFromProcessor().

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

Classes

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation