Phase retrieval from Paganin et al. 2004. More...

IPSDKIPLFILTERING_API image::ImagePtr	ipsdk::imaproc::filter::dicPhaseRetrieval2dImg (const image::ImageConstPtr &pInImg, const ipReal32 inStdDev)
	wrapper function for Phase retrieval from Paganin et al. 2004 More...

IPSDKIPLFILTERING_API image::ImagePtr	ipsdk::imaproc::filter::dicPhaseRetrieval2dImg (const image::ImageConstPtr &pInImg, const ipReal32 inStdDev, const ipReal64 mu, const ipReal64 delta, const ipReal64 defocusDistance)
	wrapper function for Phase retrieval from Paganin et al. 2004 More...

IPSDKIPLFILTERING_API image::ImagePtr	ipsdk::imaproc::filter::dicPhaseRetrieval2dImg (const image::ImageConstPtr &pInImg, const ipReal32 inStdDev, const ipReal64 mu, const ipReal64 delta, const ipReal64 defocusDistance, const ipReal64 lambda, const ipReal64 lengthScale, const ipReal64 energy)
	wrapper function for Phase retrieval from Paganin et al. 2004 More...

IPSDKIPLFILTERING_API void	ipsdk::imaproc::filter::dicPhaseRetrieval2dImg (const image::ImageConstPtr &pInImg, const ipReal32 inStdDev, const image::ImagePtr &pOutImg)
	wrapper function for Phase retrieval from Paganin et al. 2004 More...

IPSDKIPLFILTERING_API void	ipsdk::imaproc::filter::dicPhaseRetrieval2dImg (const image::ImageConstPtr &pInImg, const ipReal32 inStdDev, const ipReal64 mu, const ipReal64 delta, const ipReal64 defocusDistance, const image::ImagePtr &pOutImg)
	wrapper function for Phase retrieval from Paganin et al. 2004 More...

IPSDKIPLFILTERING_API void	ipsdk::imaproc::filter::dicPhaseRetrieval2dImg (const image::ImageConstPtr &pInImg, const ipReal32 inStdDev, const ipReal64 mu, const ipReal64 delta, const ipReal64 defocusDistance, const ipReal64 lambda, const ipReal64 lengthScale, const ipReal64 energy, const image::ImagePtr &pOutImg)
	wrapper function for Phase retrieval from Paganin et al. 2004 More...

Detailed Description

Phase retrieval from Paganin et al. 2004.

This algorithm is an implementation of Paganin's phase retrieval [1], used for Laplacian microscope imaging.

The calculation can be expressed by using the following formula:

$\phi[\textbf{x}] = -\frac{\delta}{\beta}ln\left(\mathcal{F}^{-1}\left( \frac{\mathcal{F} \left( I[\textbf{x}]/I_0[\textbf{x}] \right)}{F \frac{\delta}{\beta}\pi\left| \textbf{v} \right|^2 + 1} \right)\right)$

where $I[\textbf{x}]$ and $\phi[\textbf{x}]$ are respectively the input and the result images at the coordinates $\textbf{x}$ . $I_0[\textbf{x}]$ is the input image $I[\textbf{x}]$ smoothed by a Gaussian filter with standard deviation InStdDev. $\mathcal{F}$ is the Fourier transform operator, $\textbf{v}$ is the coordinates in the frequency domain, in $[-0.5, 0.5]^2$ and $F$ is the Fresnel number, calculated as:.

$F = \frac{defocusDist \times \lambda}{lengthscale^2}$

By default the wavelength $\lambda$ is defined as $\lambda = \frac{12.4 \times 10^{-10}}{E}$ and $E$ is the energy, witch equals 13 by default, as suggested in the PyPhase implementation [2].

The other parameters are related to the microscope specifications:

$\mu$ is the absorption coefficient,
$\delta$ is related to the refractive index (which equals $1-\delta$ ),
is the defocus distance used for the acquisition,
$\beta = \frac{\mu \lambda}{4 \pi}$ ,
is the scale used to define the parameters representing lengths (i.e. $\mu$ , $\lambda$ and )

Note: This algorithm and the Differential Interference Contrast (DIC) Integration 2D algorithm have different application. The Differential Interference Contrast (DIC) Integration 2D needs an oriented gradient as input image, whereas the phase retrieval algorithm uses an image acquired from a Laplacian microscope.

[1] Paganin D, Gureyev TE, Mayo SC, Stevenson AW, Nesterets YI, Wilkins SW. X-ray omni microscopy. J Microsc. 2004 Jun

[2] https://gitlab.in2p3.fr/mlanger/pyPhase/-/tree/master

Attributes description

Attribute description for algorithm :

Name	ToolTip	Default Initializer
ipsdk::imaproc::attr::InImg	[Input] image for processing operation	X
ipsdk::imaproc::attr::InStdDev	[Input] standard deviation used for operation along all axis	X
ipsdk::imaproc::filter::InDicPhaseRetrievalParams	[Input] Attribute for the set of parameter used for the DIC phase retrieval algorithm	X
ipsdk::imaproc::attr::OutWk1RealImg	[Output] Temporary working image for algorithm	ipsdk::imaproc::duplicateInOut (_pOutWk1RealImg, _pInImg, ipsdk::image::eImageBufferType::eIBT_Real32)
ipsdk::imaproc::attr::OutWk2RealImg	[Output] Temporary working image for algorithm	ipsdk::imaproc::duplicateInOut (_pOutWk2RealImg, _pInImg, ipsdk::image::eImageBufferType::eIBT_Real32)
ipsdk::imaproc::attr::OutRealImg	[Output] image for processing operation (data contained in image buffer are reals)	ipsdk::imaproc::duplicateInOut (_pOutRealImg, _pInImg, ipsdk::image::eImageBufferType::eIBT_Real32)

Global Rule description

Global rule description for algorithm :
ipsdk::imaproc::matchSize (_pInImg,_pOutWk1RealImg) &&
ipsdk::imaproc::matchSize (_pInImg,_pOutWk2RealImg) &&
ipsdk::imaproc::matchSize (_pInImg,_pOutRealImg)

Example of Python code :

Example imports

import PyIPSDK

import PyIPSDK.IPSDKIPLFiltering as filter

Code Example

    # opening of input images
    inImg = PyIPSDK.loadTiffImageFile(inputImgPath)
    
    # Calculation
    outImg = filter.dicPhaseRetrieval2dImg(inImg, stdDev, 1000, 0.01, 0.001)

Example of C++ code :

Example informations

Associated library

IPSDKIPLFiltering

Header file

#include <IPSDKIPL/IPSDKIPLFiltering/Processor/DicPhaseRetrieval2dImg/DicPhaseRetrieval2dImg.h>

Code Example

        // opening input image
        ImagePtr pInImg = loadTiffImageFile(inImgPath);
        
        // Set the parameters
        const ipReal32 stdDev = 25.f;
        const ipReal64 mu = 1000.;
        const ipReal64 delta = 0.01;
        const ipReal64 defocusDist = 0.001;
        // compute the oriented integration
        ImagePtr pOutImg = dicPhaseRetrieval2dImg(pInImg, stdDev, mu, delta, defocusDist);

See also: DicPhaseRetrieval2dImgLvl1; DicPhaseRetrieval2dImgLvl2