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

#include <hitfinder.h>

Inheritance diagram for cass::pp208:

Collaboration diagram for cass::pp208:

Public Member Functions
	pp208 (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
enum	ColumnNames { Intensity = 0, centroidColumn = 1, centroidRow = 2, nbrOfPixels = 3, SignalToNoiseHighestPixel = 4, Index = 5, Column = 6, Row = 7, LocalBackground = 8, LocalBackgroundDeviation = 9, MaxRadius = 10, MinRadius = 11, MaxADU = 12, nUpOutliers = 13, Resolution = 14, SignalToNoiseSpot = 15, nbrOf }
	enum describing the contents of the resulting table More...

typedef result_t::storage_t	table_t
	definition of the table More...

typedef result_t::storage_t::value_type	pixelval_t
	define the type of the pixel in image More...

typedef CummulativeStatisticsNoOutlier< pixelval_t >	stat_t
	define the type of statistics used More...

typedef int64_t	index_t
	define the index in the image More...

typedef std::pair< index_t, index_t >	shape_t
	define the shape of the image More...

typedef std::vector< index_t >	neighbourList_t
	define the list of neighbours More...

Protected Member Functions
int	getBoxStatistics (result_t::const_iterator pixel, const index_t linIdx, const shape_t &box, stat_t &stat)
	retrieve the box statistics More...

int	isNotHighest (result_t::const_iterator pixel, const index_t linIdx, shape_t box, stat_t &stat)
	check if pixel is not highest within box More...

double	lambdaFromConstant (const CASSEvent::id_t &)
	retrieve the constant wavelength More...

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

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

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

pixelval_t	thresholdFromProcessor (const CASSEvent::id_t &id)
	retrieve the threshold from the processor More...

pixelval_t	thresholdFromConstant (const CASSEvent::id_t &id)
	retrieve the threshold constant 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
	processor containing the image to find the bragg peaks in More...

shape_t	_box
	the size of the box within which the peak should lie More...

shape_t	_section
	size of a image section More...

shape_t	_imageShape
	size of the incomming image More...

stat_t::value_type	_minSnr
	minimum Signal to Noise Ratio thats is needed for a pixel to be an outlier More...

float	_minRatio
	minimum ratio of nbr of points used for statistics to nbr of outliers More...

stat_t::count_type	_minNbrPixels
	the minimum nbr of pixels in the bragg peak More...

neighbourList_t	_neighbourOffsets
	the list of offsets to next neighbours More...

std::vector< double >	_src2labradius
	the conversion table from raw to lab 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 &)>	_getLambda
	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 &)>	_getDistance
	function that gets the detectordistance More...

pixelval_t	_threshold
	pixel threshold to be exceeded More...

shared_pointer	_threshPP
	pp containing threshold in case its not fixed More...

std::tr1::function< pixelval_t(const CASSEvent::id_t &)>	_thresh
	function that gets the detectordistance 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

find bragg peaks and store them in list

Available PostProcessors:: "208": find bragg peaks and store them in list

Finds bragg peaks by checking how many pixels that are connected are above the given singal to noise ratio. The mean and standart deviation for calculating the SNR is determined by a local box size. Here the statistics is cleaned from the outliers so that pixels that are potentially part of the peak are not included in the background and stdv calculation. If the ratio between outliers of the distribution and pixel that are part of the distribution does not satisfy the user setting, the box size will be increased and the process to determine the local background and std is repeated.

This algorithm was inspired by an algorithm described in Zhang et al. J. Appl. Cryst. (2006). 39, 112-119 [ doi:10.1107/S0021889805040677 ]

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%/{BraggPeakDiameter}
Minimum Diameter of a Bragg Peak. Used for determining the optimal box size and nbr of pixels in the Bragg Peak. Default is 2.

Processor/%name%/{MinRatio}
The minimum ratio of pixel that are outliers of the distribution in the box to the pixels that are part of the distribution in the box. 3 mean that there have to be at least 3 times as meany pixels that are part of the distribution than outliers of the distribution. Default is 3.

Processor/%name%/{Threshold}
Threshold of pixel in adu to be exeeded. Can also be the name of a Processor that contains the Threshold value.

Processor/%name%/{MinSignalToNoiseRatio}
Signal to noise ratio of a pixel. Value needs to be exceeded in order for the pixel to be part of a bragg peak. Default is 4.

Processor/%name%/{MinNbrPixels}
Minimum Nbr of Pixels to be part of a Bragg Peak. Default is determined by BraggPeakRadius. $nbr = (2 \times BraggPeakRadius)^2$

Processor/%name%/{BoxSizeX|BoxSizeY}
col (x) and rows (y) of the box that is used for determining the background. The box is going from -BoxSizeX ... BoxSizeX in x and same in y. Default is determined by the BraggPeakRadius. $size = \sqrt{\pi} \times BraggPeakRadius$

Processor/%name%/{GeometryFilename}
The geom file to use. Default is "wrong_file" in which case the resolution will be calculated completely wrong

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 Processor that contains the Wavelength. Default is 1.

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

Processor/%name%/{PixelSize_m}
The pixel size in m. Default is 109.92-6

Author: Lutz Foucar

Definition at line 387 of file hitfinder.h.

Member Typedef Documentation

typedef int64_t cass::pp208::index_t

protected

define the index in the image

Definition at line 413 of file hitfinder.h.

typedef std::vector<index_t> cass::pp208::neighbourList_t

protected

define the list of neighbours

Definition at line 419 of file hitfinder.h.

typedef result_t::storage_t::value_type cass::pp208::pixelval_t

protected

define the type of the pixel in image

Definition at line 407 of file hitfinder.h.

typedef std::pair<index_t,index_t> cass::pp208::shape_t

protected

define the shape of the image

Definition at line 416 of file hitfinder.h.

typedef CummulativeStatisticsNoOutlier<pixelval_t> cass::pp208::stat_t

protected

define the type of statistics used

Definition at line 410 of file hitfinder.h.

typedef result_t::storage_t cass::pp208::table_t

protected

definition of the table

Definition at line 404 of file hitfinder.h.

Member Enumeration Documentation

enum cass::pp208::ColumnNames

protected

enum describing the contents of the resulting table

Enumerator
Intensity
centroidColumn
centroidRow
nbrOfPixels
SignalToNoiseHighestPixel
Index
Column
Row
LocalBackground
LocalBackgroundDeviation
MaxRadius
MinRadius
MaxADU
nUpOutliers
Resolution
SignalToNoiseSpot
nbrOf

Definition at line 422 of file hitfinder.h.

Constructor & Destructor Documentation

pp208::pp208 ( const name_t & name )

constructor

Definition at line 690 of file hitfinder.cpp.

References loadSettings().

Member Function Documentation

double cass::pp208::distanceFromConstant ( const CASSEvent::id_t & )

inlineprotected

retrieve the constant detector distance

Parameters

id unused

Definition at line 489 of file hitfinder.h.

References _detdist.

Referenced by loadSettings().

double pp208::distanceFromProcessor ( 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 888 of file hitfinder.cpp.

References _detdistPP.

Referenced by loadSettings().

int pp208::getBoxStatistics	(	result_t::const_iterator	pixel,
		const index_t	linIdx,
		const shape_t &	box,
		stat_t &	stat
	)

protected

retrieve the box statistics

Details:

Returns: 0 when all non bad pixels have been added to the statistics. 1 if one of the pixels in the box was higher than the center pixel

Parameters

pixel	const iterator to the center pixel
linIdx	the linearized index of the pixel
box	the shape of the box to check
stat	the statistics calculator used to determine mean and stdv of pixels in box

get coordinates of pixel from the linearized index

make sure that pixel is located such that the box will not conflict with the image and section boundaries. If it does continue with next pixel

go through all pixels defined by the box from -rows ... rows, -cols ... cols

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

if its not a bad pixel add pixel to statistics

Definition at line 907 of file hitfinder.cpp.

References _imageShape, _section, cass::CummulativeStatisticsNoOutlier< Type >::addDatum(), and use.

Referenced by isNotHighest().

int pp208::isNotHighest	(	result_t::const_iterator	pixel,
		const index_t	linIdx,
		shape_t	box,
		stat_t &	stat
	)

protected

check if pixel is not highest within box

Details:

Returns: 0 if pixel is heighest, 1 otherwise

Parameters

pixel	const iterator to the pixel to be checked
linIdx	the linearized index of the pixel
box	the shape of the box to be checked (cols x rows)
stat	the statistics calculator used to determine mean and stdv of pixels in box

check whether current pixel value is highest and generate background values

increase the box size and start over if the fraction of outliers to points used in the statistics is smaller than requested.

skip this pixel if there are not enough pixels that could potentially be part of the bragg peak.

Definition at line 946 of file hitfinder.cpp.

References _minNbrPixels, _minRatio, getBoxStatistics(), cass::CummulativeStatisticsNoOutlier< Type >::nbrPointsUsed(), cass::CummulativeStatisticsNoOutlier< Type >::nbrUpperOutliers(), cass::CummulativeStatisticsNoOutlier< Type >::reset(), and use.

Referenced by process().

double cass::pp208::lambdaFromConstant ( const CASSEvent::id_t & )

inlineprotected

retrieve the constant wavelength

Parameters

id unused

Definition at line 477 of file hitfinder.h.

References _wavelength.

Referenced by loadSettings().

double pp208::lambdaFromProcessor ( 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 881 of file hitfinder.cpp.

References _wavelengthPP.

Referenced by loadSettings().

void pp208::loadSettings ( size_t )

virtual

load the settings of this pp

area of box should at least be ratio times area of peak.

$\begin{eqnarray*} A_{box}&=& ratio \times A_{circle} \\ size^2 &=& ratio \times \pi r^2 \\ size &=& \sqrt{\pi r^2 \times ratio} \\ &=& r \sqrt{\pi \times ratio} \\ &=& 0.5 d \sqrt{\pi \times ratio} \end{eqnarray*}$

If $ size $ goes from $-s ... s$ then $ size = 2s+1 $

$\begin{eqnarray*} 2s + 1 &=& 0.5 d \sqrt{\pi \times ratio} \\ s &=& 0.5 \times 0.5 d \sqrt{\pi \times ratio} - 0.5 \\ &=& 0.25 d \sqrt{\pi \times ratio} - 0.5 \end{eqnarray*}$

convert to integer

$\begin{eqnarray*} (int)s &=& 0.25d\sqrt{\pi \times ratio} - 0.5 + 0.5 \\ &=& 0.25d\sqrt{\pi \times ratio} \end{eqnarray*}$

min nbr of pixels should reflect the area under the bragg peak $nbrPeaks = 0.25 \pi d$

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

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

check if the input processors have the correct type

generate the lookuptable for the radia, if no geom file is provided, set the radia to 0

set up the neighbouroffset list

Create the result output

log what the user was requesting

Reimplemented from cass::Processor.

Definition at line 697 of file hitfinder.cpp.

References _box, cass::Processor::_condition, _detdist, _detdistPP, _getDistance, _getLambda, _imagePP, _imageShape, _minNbrPixels, _minRatio, _minSnr, _neighbourOffsets, _section, _src2labradius, _thresh, _threshold, _threshPP, _wavelength, _wavelengthPP, cass::Log::add(), QSettings::beginGroup(), cass::Processor::createHistList(), distanceFromConstant(), distanceFromProcessor(), QString::fromStdString(), cass::GeometryInfo::generateConversionMap(), cass::Log::INFO, lambdaFromConstant(), lambdaFromProcessor(), cass::Processor::name(), nbrOf, cass::Processor::setupCondition(), cass::Processor::setupDependency(), cass::Processor::setupGeneral(), cass::square(), thresholdFromConstant(), thresholdFromProcessor(), cass::toString(), QSettings::value(), cass::ACQIRIS::x, and cass::ACQIRIS::y.

Referenced by pp208().

void pp208::process	(	const CASSEvent &	evt,
		result_t &	result
	)

virtual

process event

clear the resulting table to fill it with the values of this image

get a table row that we can later add to the table

set up a mask that we can see which pixels have been treated

get iterators for the mask and the image with which we can iterate through the image, also rember which linearized index we are working on right now, to be able to retrieve the column and row that the current pixel corresponsed to.

check if pixel should be treated, when it has been treated before continue with the next pixel

check if pixel is above the threshold, otherwise continue with the next pixel

check if pixel is highest within box. If so, check if there are enough pixels that are not outliers. If there are not enough pixels in the box increase the box size and do the checks all over again. If the pixel is not highest within the bigger box continue with the next pixel.

retrive statistical values from the calculator

get coordinates of pixel in image from the linearized index

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.

Note: need to check if the pixel has been used after verifiying that the pixel is within the box. Otherwise in rare occasions it will happen that the pixelindex is not within the boolean array which will cause a segfault.

if the peak doesn't have enough pixels continue with next pixel

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

set the peak's properties and add peak to the list of found peaks

tell that only the result of one event (image) is present in the table

Reimplemented from cass::Processor.

Definition at line 985 of file hitfinder.cpp.

References _box, _getDistance, _getLambda, _imagePP, _imageShape, _minNbrPixels, _minSnr, _neighbourOffsets, _src2labradius, _thresh, cass::Result< T >::appendRows(), cass::Result< T >::begin(), centroidColumn, centroidRow, Column, cass::Result< T >::end(), cass::CASSEvent::id(), Index, cass::ACQIRIS::integral, Intensity, isNotHighest(), LocalBackground, LocalBackgroundDeviation, cass::Result< T >::lock, MaxADU, MaxRadius, cass::CummulativeStatisticsNoOutlier< Type >::mean(), MinRadius, nbrOf, nbrOfPixels, cass::CummulativeStatisticsNoOutlier< Type >::nbrUpperOutliers(), nUpOutliers, cass::Result< T >::resetTable(), Resolution, Row, SignalToNoiseHighestPixel, SignalToNoiseSpot, cass::Result< T >::size(), and cass::CummulativeStatisticsNoOutlier< Type >::stdv().