find bragg peaks and store them in a list More...

#include <hitfinder.h>

Inheritance diagram for cass::pp204:

Collaboration diagram for cass::pp204:

Public Types
enum	ColumnNames { Intensity = 0, centroidColumn = 1, centroidRow = 2, nbrOfPixels = 3, SignalToNoise = 4, Index = 5, Column = 6, Row = 7, LocalBackground = 8, LocalBackgroundDeviation = 9, nbrOfBackgroundPixels = 10, MaxRadius = 11, MinRadius = 12, MaxADU = 13, nbrOf }
	enum describing the contents of the resulting table More...

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...

Public Member Functions
	pp204 (const name_t &name)
	constructor More...

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

virtual void	loadSettings (size_t)
	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 result_t::storage_t	table_t
	definition of the table More...

typedef result_t::value_t	pixelval_t
	define the values of the pixels More...

typedef int	imagepos_t
	define the positions in the image More...

Protected Member Functions
int	getBoxStatistics (result_t::const_iterator centerPixel, const imagepos_t nColumns, pixelval_t &mean, pixelval_t &stdv, int &count)
	check highest pixel and generate the mean and standart deviation 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	_hist
	processor containing the image to find the bragg peaks in More...

std::pair< imagepos_t, imagepos_t >	_box
	the size of the box within which the peak should lie More...

std::pair< imagepos_t, imagepos_t >	_section
	size of a image section More...

float	_threshold
	pixel threshold to be exceeded More...

int	_peakRadiusSq
	the square size of bragg peak radius More...

float	_minSnr
	the min signal to noise ratio that needs to be exceeded More...

float	_minNeighbourSNR
	the min signal to noise ratio that needs to be exceeded More...

int	_minBckgndPixels
	min amount of pixels for the background calc 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...

Detailed Description

find bragg peaks and store them in a list

Available PostProcessors:: "204": find bragg peaks and store them in a list

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

User definable Parameters:

Processor/%name%/{ImageName}
the processor name that contain the 2d histogram. Default is "blubb".

Processor/%name%/{SectionSizeX|SectionSizeY}
Size of the subsection of the image. Default is 1024|512.

Processor/%name%/{BoxSizeX|BoxSizeY}
size in x and y of the box that is used for determining the median background. Default is 10|10.

Processor/%name%/{Threshold}

Processor/%name%/{MinSignalToNoiseRatio}

Processor/%name%/{MinNbrBackgrndPixels}

Processor/%name%/{BraggPeakRadius}

Author: Lutz Foucar

Definition at line 97 of file hitfinder.h.

Member Typedef Documentation

typedef int cass::pp204::imagepos_t

protected

define the positions in the image

Definition at line 142 of file hitfinder.h.

typedef result_t::value_t cass::pp204::pixelval_t

protected

define the values of the pixels

Definition at line 139 of file hitfinder.h.

typedef result_t::storage_t cass::pp204::table_t

protected

definition of the table

Definition at line 114 of file hitfinder.h.

Member Enumeration Documentation

enum cass::pp204::ColumnNames

enum describing the contents of the resulting table

Enumerator
Intensity
centroidColumn
centroidRow
nbrOfPixels
SignalToNoise
Index
Column
Row
LocalBackground
LocalBackgroundDeviation
nbrOfBackgroundPixels
MaxRadius
MinRadius
MaxADU
nbrOf

Definition at line 118 of file hitfinder.h.

Constructor & Destructor Documentation

pp204::pp204 ( const name_t & name )

constructor

Definition at line 144 of file hitfinder.cpp.

References loadSettings().

Member Function Documentation

int pp204::getBoxStatistics	(	result_t::const_iterator	centerPixel,
		const imagepos_t	nColumns,
		pixelval_t &	mean,
		pixelval_t &	stdv,
		int &	count
	)

protected

check highest pixel and generate the mean and standart deviation

function is used in SNR peak finder

Check if the center pixel is heigher than all other pixels in the box. If this is the case return 0. If there is at least one pixel whos value is higher than the center pixel return 1.

Generate the mean and standart deviation within the box around the center pixel. Only take pixels into account that are outside of the peak radius.

Returns: 0 if all pixels in the box are lower than the center pixel, 1 otherwise

Parameters

	centerPixel	iterator to the center pixel
	nColumns	the number of columns in the image
[out]	mean	contains the mean value
[out]	stdv	contains the standart deviation
[out]	count	contains the number of pixels that were used to calculate mean and stdv

only consider pixels that are not in the origin of the box

check if the current box pixel value is bigger than the center pixel value. If so skip this pixel

if box pixel is outside the radius, add it to the statistics, if it is inside the radius bad then skip, as no pixel that could potentially be part of the peak should be a bad pixel.

Definition at line 195 of file hitfinder.cpp.

References _box, _peakRadiusSq, cass::CummulativeStatisticsCalculator< Type >::addDatum(), cass::CummulativeStatisticsCalculator< Type >::count(), cass::CummulativeStatisticsCalculator< Type >::mean(), and cass::CummulativeStatisticsCalculator< Type >::stdv().

Referenced by process().

void pp204::loadSettings ( size_t )

virtual

load the settings of this pp

Create the resulting table

log what the user was requesting

Reimplemented from cass::Processor.

Definition at line 150 of file hitfinder.cpp.

References _box, cass::Processor::_condition, _hist, _minBckgndPixels, _minNeighbourSNR, _minSnr, _peakRadiusSq, _section, _threshold, cass::Log::add(), QSettings::beginGroup(), cass::Processor::createHistList(), QString::fromStdString(), cass::Log::INFO, cass::Processor::name(), nbrOf, cass::Processor::setupCondition(), cass::Processor::setupDependency(), cass::Processor::setupGeneral(), cass::toString(), and QSettings::value().

Referenced by pp204().

void pp204::process	(	const CASSEvent &	evt,
		result_t &	result
	)

virtual

process event

reset the nbr of y entries

check if pixel has been touched before

check above a set threshold

get coordinates of pixel and tell that it is touched

make sure that pixel is located such that the box will not conflict with the image and section boundaries

check wether current pixel value is highest and generate background values

check that we took more than the minimum pixels for the background

check if signal to noise ration is good for the current pixel

from the central pixel look around and see which pixels are direct part of the peak. If a neighbour is found, mask it such that one does not use it twice.

Create a list that should contain the indizes of the pixels that are part of the peak. Go through that list and check for each found neighbour whether it also has a neighbour. If so add it to the list, but only if it is part of the box.

go through all pixels in the box, find out which pixels are part of the peak and centroid them. Mask all pixels in the box as checked so one does not check them again

Reimplemented from cass::Processor.

Definition at line 235 of file hitfinder.cpp.

References _box, _hist, _minBckgndPixels, _minNeighbourSNR, _minSnr, _section, _threshold, cass::Result< T >::appendRows(), cass::Result< T >::begin(), centroidColumn, centroidRow, Column, cass::Result< T >::end(), getBoxStatistics(), cass::CASSEvent::id(), Index, cass::ACQIRIS::integral, Intensity, LocalBackground, LocalBackgroundDeviation, cass::Result< T >::lock, MaxADU, MaxRadius, MinRadius, nbrOf, nbrOfBackgroundPixels, nbrOfPixels, cass::Result< T >::resetTable(), Row, cass::Result< T >::shape(), SignalToNoise, and cass::Result< T >::size().