Determines the positions of the spectral orders, absolute or differentially, relative to a template frame. More...

Inheritance diagram for hermes.pipeline.components.measureorderpositions.measureOrderPositions:

Public Member Functions
def	__init__
	Make a Hermes component and initialize variables.

def	optionsAreValid
	check user's options, or set default values

def	__call__
	run starts here

def	checkIfItIsWorthToMeasureOrderPosition
	rapidly estimates order shift over a small part of the CCD

def	getShiftEstimateOrderModel
	return an array that contains the shift values of the order for each cross cut

def	getOrderCorrelationCoefficients
	knowing the shift interval, this method cross correlates the image with a template. More...

def	getShiftedFrame
	shift a 2D frame in the crossAxis direction inputs are the frame and the shift in pixels

def	getShiftedMask
	shift a 2D frame in the crossAxis direction inputs are the frame and the shift in pixels

def	getOrderMask
	given the shape of an order and its widths (assumed to be constant) this methods prepares a frame that will mask all the other orders. More...

Public Member Functions inherited from hermes.pipeline.core.pipelinecomponent.PipelineComponent
def	__init__

def	__call__

def	optionsAreValid

def	getOptions

def	setOptions

def	checkExistShapeUnits

def	isOption

Public Attributes
	isShiftEstimateOrderModel
	is shiftEstimateOrderModel already measured ?

	shiftStep
	The correlation step will always be equal to 1.

	isOrderShiftPrinted
	TEMPORARY? - Do we need to plot print the order shifts.

	isShiftEstimateOrderModelMeasured
	Do we need to check the shift beforehand on a smaller region ? Value is False if we have to ... More...

	isItWorthToMeasureOrderPosition
	if estimate order position provides a shift that is too large then it is not worth to measure order position

	midOrder

	midRow

	orderHalfWidth
	give the half width

	tolFastClean
	tolerance

	maxShift
	maximal shift allowed

	minShift
	minimal shift allowed

	crossAxis
	select direction

	isPolynomeBivariate
	default computation More...

	isFerosData
	Is it FEROS data == only for testing purposes.

	isDifferential

	isEstimatedAbsoluteOrderPositionsNeeded
	if at this stage absolute order positions are needed

	areVirtualEdgeOrdersAdded
	border management

	isDebug
	Set debug flag according to users needs.

	results

	xStart
	if it is needed then we have to check that the right additional input is provided More...

	xEnd
	default x end

	yStart
	default y start

	yEnd
	default y end

	optionsdict
	a global pointer needed to pass the options to estimateOrderPosition

Public Attributes inherited from hermes.pipeline.core.pipelinecomponent.PipelineComponent
	options

	logger

	ConsoleLogSeverity
	default value

	canShowGraphics
	when machine does not run matplotlib. More...

Detailed Description

Determines the positions of the spectral orders, absolute or differentially, relative to a template frame.

PURPOSE :

This module determines the positions of the spectral orders, either in
an absolute way or differentially, relative to a template frame. The
template should have in each spectral order, in cross-order direction,
profiles as close as possible to the profiles in the input frame (inclusive
the presence or absence of a background). Measurement errors caused by a
different discretisation of the data are minimized by the use of an algorithm
developed by David & Verschueren (1995, A&A, 111, 183). The larger the number
of (trustworthy) cross-cuts used, the higher the precision obtainable in the
modelBackground module.

A useful indicator of how trustworthy the result is (in other words, to what
extent the input and template data are similar in cross-order shape) can be
obtained from the correlation coefficient between input and template cross-order
profile as compared to the signal-to-noise ratio (and the difference in
discretisation of the cross-order profile). Only trustworthy data will be passed
to modelOrderPosition. Suspects cross-cuts (known hot or dark pixels, radiation
events detected through a too low correlation coefficient, cross-cuts well outside
the useful zone of the spectral orders) are marked.




COMMENTS : (1) Auto-correlation of the (shifted) template with itself
(for each constant-wavelength bin in each spectral order) should be
computed when choosing the instrument model.
Any moment that the template or the mask vector defining the
extraction slit for each order, or the shift range is changed
(the shift range should never be changed, unless the basic measurement
method for estimating the centre of the cross-correlation peak is
modified), this auto-correlation has to be re-computed.
The auto-correlation for the image with itself is computed out of the
loop over the different shifts.




SYNTAX :
measureOrderPositions(self, instrumentModel)




INPUT CONSTANTS FROM INSTRUMENT MODEL :


referenceFrame
    Is the modelFlatField image. The path and name of the file could
    be written in the InstrumentConfig.xml file. In that case we should
    decide if the modelFlatField is loaded once for all in the begining
    of the chain, or if it has to be loaded each time we need it in a
    component.
    May be we could foresee a Model.xml file. It could be loaded at
    the beginning by a component named e.g. modelLoader that would prepare
    the InputDict in a way depending on the chain composition or the options.
templateorderpositionscoefficients
    Are the polynomial coefficients that define the shape of orders of the
    modelFlatField image. Since we are using FEROS data it is loaded for
    the moment by a Ferosinitchain component saved in the utilities package.




INPUT DATA FROM RESULTDICT :

MANDATORY :
    imageFrame
        Input image frame. It is supposed to be a single file.



OPTIONS READ FROM OPTIONDICT :

MANDATORY :
    maxShiftEstimateOrderModel
        Is the upper boundary of the allowed template shifts.
        Could be written in the InstrumentConfig.
    minShiftEstimateOrderModel
        Is the lower boundary of the allowed template shifts.
        Could be written in the InstrumentConfig.
    crossAxis
        Is the cross order axis. Its value is 1 or 0.
        Could be written in the InstrumentConfig.
    orderHalfWidth
        Half Width of the orders in pixel units. This something that
        should be related to the modelFlatField image.

OPTIONAL :
    For the moment, when self.isShiftEstimateOrderModelMeasured = False
    the component first launches the estimateOrderPosition component.
    In that case, the following options should also be set.

    isDebug (boolean)
        default is True
        When debug information is needed than this parameter should be True.
        When the parameter is set to True you will find in the self.results["DebugPath"]
    the following fits files: ...

    isFerosData (boolean)
        default is False
        Tells whether we are using FEROS data.
    tolFastClean
        Is the tolerance for the fast cleaning of the frame subregion
        we want to cross-correlate. All pixels having an intensity
        higher than tolFastClean are masked.
    xStart
        Definition of the frame subregion. It is the X lower edge
        of the subregion. Definition of X and Y depends for the moment
        on the crossAxis value. May be this is stupid ?
        Could be set in the InstrumentConfig file or Model.xml file.
    xEnd
        Definition of the frame subregion. It is the X upper edge
        of the subregion. Definition of X and Y depends for the moment
        on the crossAxis value. May be this is stupid ?
        Could be set in the InstrumentConfig file or Model.xml file.
    yStart
        Definition of the frame subregion. It is the Y lower edge
        of the subregion. Definition of X and Y depends for the moment
        on the crossAxis value. May be this is stupid ?
        Could be set in the InstrumentConfig file or Model.xml file.
    yEnd
        Definition of the frame subregion. It is the Y upper edge
        of the subregion. Definition of X and Y depends for the moment
        on the crossAxis value. May be this is stupid ?
        Could be set in the InstrumentConfig file or Model.xml file.
    areVirtualEdgeOrdersAdded
        default : True
        Do we have to foresee additional edge orders ?


OUTPUT written to the InputDict :

MeasuredRelativeOrderPositions
    Is an array of NxM order shifts. M is the number of orders
    and N is the number of rows/columns.
AbsoluteOrderPositionsInTemplate
    Is a NxM frame, where M is the order index and N the row/column index, that
    contains the column/row index of the center of the orders.


NOTE :
If you have the following error:
    finin = (image * image * mask).sum(axis = 1)
    TypeError: sum() got an unexpected keyword argument 'axis'
It probably means that you are using an older version of pyfits.

Member Function Documentation

def hermes.pipeline.components.measureorderpositions.measureOrderPositions.getOrderCorrelationCoefficients	(	self,
		image,
		template,
		mask
	)

knowing the shift interval, this method cross correlates the image with a template.

A mask is used to only cross-correlate a given order.

def hermes.pipeline.components.measureorderpositions.measureOrderPositions.getOrderMask	(	self,
		frame,
		orderCoefficients,
		orderHalfWidth,
		order,
		bivarianceDegree
	)

given the shape of an order and its widths (assumed to be constant) this methods prepares a frame that will mask all the other orders.

orderCoefficients: polynomial coefficients array that describes the order shape orderHalfWidth (in pixels)

Member Data Documentation

hermes.pipeline.components.measureorderpositions.measureOrderPositions.isPolynomeBivariate

default computation

computation model

hermes.pipeline.components.measureorderpositions.measureOrderPositions.isShiftEstimateOrderModelMeasured

Do we need to check the shift beforehand on a smaller region ? Value is False if we have to ...

hermes.pipeline.components.measureorderpositions.measureOrderPositions.xStart

if it is needed then we have to check that the right additional input is provided

default x start

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

pipeline/components/measureorderpositions.py

Public Member Functions

Public Attributes

Detailed Description

Member Function Documentation

Member Data Documentation