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Last modified: Thu Jan 17 15:40:39 2013.


List of Routines


Routine Descriptions

CXS_GET_ROUND_SUPPORT

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 NAME:
       CXS_GET_ROUND_SUPPORT

 PURPOSE: 
       This function will return a simple array with a central
       circular region where each element has the value 1.0. Outside
       the value returned is zero. This function has been written to
       allow each create of the support array. For example when
       reconstructing the white-field for Fresnel CDI reconstruction.
       Note that it does not actually call any method from the cxs
       software library.

 CALLING SEQUENCE:

	CXS_GET_ROUND_SUPPORT, nx, ny, radius

 INPUTS:

       n_x: 
             The number of pixels in the horizontal direction of the
             output array.
       n_y: 
             The number of pixels in the vertical direction of the
             output array.
       radius: 
             The radius of the circle in pixels.

 RETURN:
       A two dimensional array which can be used to set the support
       for any of the CDI reconstructions.

 EXAMPLE:

       cxs_get_round_support, 1024, 1024, 0.25*1024

(See /data/DIXE/dixe/trunk/cxs_software/interfaces/idl/CXS_interface.pro)


CXS_INIT_FRESNEL

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 NAME:
       CXS_INIT_FRESNEL

 PURPOSE:
       Set-up a Fresnel CDI reconstruction. This will
       initialise the reconstruction using a previously reconstructed
       white-field, detector data, sample support and experimental 
       parameters. Some defaults will be set and memory will be
       allocated ready for reconstructing the sample
       exit-surface-wave. It is necessary to call this procedure before
       attempting to call any of the reconstruction methods
       (e.g. before setting the algorithm or calling CXS_ITERATE).

       Calling this procedure will initialise the reconstruction algorithm
       to the error-reduction with a relaxation parameter of 0.9.

 CALLING SEQUENCE:

	CXS_INIT_FRESNEL, data, support, white-field, beam_wavelength,
	                  focal_detector_length, focal_sample_length, 
                         pixel_size [, normalisation, starting_point ]

 INPUTS:

       You may use any length units for the experimental parameters
       below, as long as all quantities are given in the same units.

	data: 
             The detector data with the sample in place. It should be
             in the form of a 2D array.

       support: 
             A 2D array of integers or doubles which give the sample support.
             Values or 1 or greater are considered inside
             the support. All others are considered to be
             outside the support.

       white-field:
             A COMPLEX 2D array of the reconstructed white-field in
             the detector plane. This can be recovered using 
             CXS_INIT_FRESNEL_WF followed by CXS_ITERATE.

       beam_wavelength:
             The beam wavelength.

       focal_detector_length:
             The distance between the focal point and the detector.

       focal_sample_length:
             The distance between the focal point and the sample.

       pixel_size:
             The side length of one detector pixel.

       normalisation: 
             The factor to scale the white-field before
             performing FCDI. If this parameter is excluded, the
             ratio of the square-root of the intensity data and the
             white-field magnitude is used as the normalisation.

       starting_point: 
             As an option you may supply an initial 
             guess of the exit-surface-wave for the sample. 
             This maybe useful, for example, if you wish to 
             start from the end point of a previous run. The
             format of this parameter much be a 2D array of
             COMPLEX variables. If this parameter is not supplied,
             the initialisation described in Harry's review paper: 
             page 29. (in particular e.q. 137) is used.

 EXAMPLE:

        cxs_init_fresnel, my_data, my_supports, my_white-field, $
                          4.892e-10, 0.9078777, 2.16e-3, $
                          13.5e-6

(See /data/DIXE/dixe/trunk/cxs_software/interfaces/idl/CXS_interface.pro)


CXS_INIT_FRESNEL_WF

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 NAME:
       CXS_INIT_FRESNEL_WF

 PURPOSE:
       Set-up a Fresnel white-field CDI reconstruction. This will
       initialise the reconstruction with the white-field intensity, 
       zone-plate support and experimental parameters. Some defaults 
       will be set and memory will be allocated ready for 
       reconstructing the white-field (phase and magnitude) in the
       detector plane. It is necessary to call this procedure before
       attempting to call any of the reconstruction methods
       (e.g. before setting the algorithm or calling CXS_ITERATE).

 CALLING SEQUENCE:

	CXS_INIT_FRESNEL_WF, data, support, beam_wavelength,
                            zone_focal_length, focal_detector_length,
                            pixel_size [,starting_point]

 INPUTS:

       You may use any length units for the experimental parameters
       below, as long as all quantities are given in the same units.

	data: 
             The white-field illumination. It should be
             in the form of a 2D array.

       support: 
             A 2D array of integers or doubles giving the zone-plate support.
             Values or 1 or greater are considered inside
             the support. All others are considered to be
             outside the support.

       beam_wavelength:
             The beam wavelength.

       zone_focal_length:
             The distance between the zone plate and the focal point.

       focal_detector_length:
             The distance between the focal point and the detector.

       pixel_size:
             The side length of one detector pixel.

       starting_point: 
             As an option you may supply an initial guess of the 
             white-field. This may be useful, for example, if you 
             wish to start from the end point of a previous run. The
             format of this parameter must be a 2D array of
             COMPLEX variables. If this parameter is not supplied,
             the starting point is initialised to be zero outside
             the support, a random number inside the support 
             for the magnitude and zero for the phase.

 EXAMPLE:

        An example of loading two 2D arrays from file and using
        them to initialise the white-field reconstruction for FCDI:

        my_support = cxs_read_tiff(1024,1024,'support.tiff')
        my_data = cxs_read_tiff(1024,1024,'data.tiff')
        cxs_init_fresnel_wf, my_data, my_support, 4.892e-10, 16.353e-3, 0.9078777,13.5e-6

(See /data/DIXE/dixe/trunk/cxs_software/interfaces/idl/CXS_interface.pro)


CXS_INIT_PARTIAL

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 NAME:
       CXS_INIT_PARTIAL

 PURPOSE:
       Set-up a Partial CDI reconstruction. This will
       initialise the reconstruction with sample support and experimental 
       parameters. Some defaults will be set and memory will be
       allocated ready for reconstructing the sample
       exit-surface-wave. It is necessary to call this procedure before
       attempting to call any of the reconstruction methods
       (e.g. before setting the algorithm or calling CXS_ITERATE).

       Calling this procedure will initialise the reconstruction algorithm
       to the error-reduction with a relaxation parameter of 0.9.

 CALLING SEQUENCE:

 CXS_INIT_PARTIAL, data, support, beta, lcx, lcy, pxsize, pysize, beam_energy
                   zsd [, starting_point ]

 INPUTS:

       Please use metres for the lengths, and eV for the energy.

       data: 
             The detector data with the sample in place. It should be
             in the form of a 2D array.

       support: 
             A 2D array of integers or doubles which give the sample support.
             Values or 1 or greater are considered inside
             the support. All others are considered to be
             outside the support.

       beta:
             The relaxation parameter.
             
       lcx:
             The coherence length in the x direction
             
       lcy:
             The coherence length in the y direction

       pxsize:
             The size of the detector pixel in the x direction

       pysize:
             The size of the detector pixel in the y direction

       beam energy: 
             The beam energy in eV

       starting_point: 
             As an option you may supply an initial 
             guess of the exit-surface-wave for the sample. 
             This maybe useful, for example, if you wish to 
             start from the end point of a previous run. The
             format of this parameter much be a 2D array of
             COMPLEX variables. If this parameter is not supplied,
             the initialisation described in Harry's review paper: 
             page 29. (in particular e.q. 137) is used.

 EXAMPLE:

        cxs_init_fresnel, my_data, my_supports, my_white-field, $
                          4.892e-10, 0.9078777, 2.16e-3, $
                          13.5e-6

(See /data/DIXE/dixe/trunk/cxs_software/interfaces/idl/CXS_interface.pro)


CXS_INIT_PLANAR

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 NAME:
       CXS_INIT_PLANAR

 PURPOSE:
       Set-up a planar CDI reconstruction. This will
       initialise the reconstruction with the data
       and support. Some defaults will be set and
       memory will be allocated ready for reconstruction.
       It is necessary to call this procedure before
       attempting to call any of the reconstruction methods
       (e.g. before setting the algorithm or 
       calling CXS_ITERATE).

       Calling this procedure will initialise the reconstruction 
       algorithm to hybrid-input-output with a relaxation parameter of 0.9.


 CALLING SEQUENCE:

	CXS_INIT_PLANAR, Data, Support [,Starting_point]


 INPUTS:

	Data: 
             The detector illumination. It should be
             in the form of a 2D array

       Support: 
             A 2D Array giving the sample support.
             Values or 1 or greater are considered inside
             the support. All others are considered to be
             outside the support.

       Starting_point: 
             As an option you may supply an initial 
             guess of the exit-surface-wave for the sample. 
             This maybe useful, for example, if you wish to 
             start from the end point of a previous run. The
             format of this parameter much be a 2D array of
             COMPLEX variables. If this parameter is not supplied,
             the starting point is initialised to be zero outside
             the support and a random number inside the support, 
             for both the magnitude and phase.

 EXAMPLE:
        An example of loading two 2D arrays from file and using
        them to initialise the planar reconstruction:

        my_support = cxs_read_tiff(1024,1024,'planar_support.tiff')
        my_data = cxs_read_tiff(1024,1024,'planar_data.tiff')
        CXS_INIT_PLANAR, my_data, my_support

(See /data/DIXE/dixe/trunk/cxs_software/interfaces/idl/CXS_interface.pro)


CXS_INIT_POLY

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 NAME:
       CXS_INIT_POLY

 PURPOSE:
       Set-up a Polychromatic CDI reconstruction. This will
       initialise the reconstruction with sample support and experimental 
       parameters. Some defaults will be set and memory will be
       allocated ready for reconstructing the sample
       exit-surface-wave. It is necessary to call this procedure before
       attempting to call any of the reconstruction methods
       (e.g. before setting the algorithm or calling CXS_ITERATE).

       Calling this procedure will initialise the reconstruction algorithm
       to the error-reduction with a relaxation parameter of 0.9.

 CALLING SEQUENCE:

 CXS_INIT_PARTIAL, data, support, beta, [, starting_point ]

 INPUTS:

       Please use metres for the lengths, and eV for the energy.

       data: 
             The detector data with the sample in place. It should be
             in the form of a 2D array.

       support: 
             A 2D array of integers or doubles which give the sample support.
             Values or 1 or greater are considered inside
             the support. All others are considered to be
             outside the support.

       beta:
             The relaxation parameter.
	
       starting_point: 
             As an option you may supply an initial 
             guess of the exit-surface-wave for the sample. 
             This maybe useful, for example, if you wish to 
             start from the end point of a previous run. The
             format of this parameter much be a 2D array of
             COMPLEX variables. If this parameter is not supplied,
             the initialisation described in Harry's review paper: 
             page 29. (in particular e.q. 137) is used.

 EXAMPLE:

        cxs_init_fresnel, my_data, my_supports

(See /data/DIXE/dixe/trunk/cxs_software/interfaces/idl/CXS_interface.pro)


CXS_SET_BEAM_STOP

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 NAME:
       CXS_SET_BEAM_STOP

 PURPOSE: 
       For PlanarCDI, you may set the beam stop region in the
       detector plane. This region will be left to float (i.e. left
       unscaled) when the intensity scaling in performed. Zeros in
       the array (which is passed) indicate the beam-stop region,
       all other values indicate that those pixel should be scaled.

 CALLING SEQUENCE:

	CXS_SET_BEAM_STOP, beam_stop_region

 INPUTS:

       beam_stop_region: 
             A 2D array of doubles or integers. Values of 0 are
             considered inside the beam-stop region. All others are
             considered to be outside the beam-stop region.

 EXAMPLE:

       cxs_set_beam_stop, my_beam_stop_region

(See /data/DIXE/dixe/trunk/cxs_software/interfaces/idl/CXS_interface.pro)


CXS_SET_INTENSITY

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 NAME:
       CXS_SET_INTENSITY

 PURPOSE:
       Set the detector intensity data. This will override 
       the intensity given to any of the CXS_INIT methods.
       In general, users should not need to call this method.

 CALLING SEQUENCE:

	CXS_SET_INTENSITY, data

 INPUTS:

       data: 
             The detector data. It should be in the form of a 2D
             array or doubles or integers.


 EXAMPLE:

       cxs_set_intensity, my_data

(See /data/DIXE/dixe/trunk/cxs_software/interfaces/idl/CXS_interface.pro)


CXS_SET_SUPPORT

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 NAME:
       CXS_SET_SUPPORT

 PURPOSE:
       SET THE SUPPORT SHAPE TO BE USED IN RECONSTRUCTION. THIS WITH OVERRIDE 
       THE SUPPORT GIVEN TO ANY OF THE CXS_INIT METHODS AND MAYBE CALLED
       AT ANY TIME DURING THE RECONSTRUCTION.  

 CALLING SEQUENCE:

	CXS_SET_SUPPORT, SUPPORT

 INPUTS:

       SUPPORT: 
             A 2D ARRAY OF DOUBLES OR INTEGERS GIVING THE SAMPLE'S 
             (OR ZONE-PLATE'S) SUPPORT. VALUES OF 1 OR GREATER ARE 
             CONSIDERED INSIDE THE SUPPORT. ALL OTHERS ARE CONSIDERED 
             TO BE OUTSIDE THE SUPPORT.

 EXAMPLE:

       CXS_SET_SUPPORT, MY_SUPPORT

(See /data/DIXE/dixe/trunk/cxs_software/interfaces/idl/CXS_interface.pro)