├── LICENSE ├── README.md ├── code ├── data │ ├── beads.mat │ ├── beads_param.m │ ├── sh.mat │ ├── sh_param.m │ ├── twopoint_3d.mat │ ├── twopoint_x_3d.mat │ ├── twopoint_x_param.m │ ├── twopoint_z_3d.mat │ └── twopoint_z_param.m ├── function │ ├── 3d obj │ │ ├── circHelix.m │ │ ├── conHelix.m │ │ └── randomScatter.m │ ├── L1phi.m │ ├── LinOpConv1.m │ ├── LinOpWavePropKernel.m │ ├── OTF3D.m │ ├── TVphi.m │ ├── TVpsi.m │ ├── TwIST.m │ ├── VecProp3D.m │ ├── dispPlotCmp.m │ ├── iVecProp3D.m │ ├── setData.m │ ├── setData.m~ │ ├── setHoloData.m │ ├── utils │ │ ├── C2V.m │ │ ├── CGwrapper.m │ │ ├── Diver3D.m │ │ ├── Grad3D.m │ │ ├── MatProp3D.m │ │ ├── PlotMult.m │ │ ├── V2C.m │ │ ├── callcounter.m │ │ ├── evar.m │ │ ├── ftvcs_al_TVL2p.m │ │ ├── ftvcs_al_opts.m │ │ ├── ftvcs_alp.m │ │ ├── helinmatrix.m │ │ ├── holoNorm.m │ │ ├── holoResize.m │ │ ├── holodenoise.m │ │ ├── iMatProp3D.m │ │ ├── noiseAnalysis.m │ │ ├── plotdatacube.m │ │ ├── posdet.m │ │ ├── selectline.m │ │ ├── show3d.m │ │ ├── view3d.m │ │ ├── vol3d.m │ │ └── write3d.m │ └── volObjGen.m ├── main_exp.m ├── main_sim_Cpx.m ├── main_sim_Inten.m ├── reference │ ├── 3d HIO DNA │ │ ├── FT3Dc.m │ │ ├── IFT3Dc.m │ │ ├── README.txt │ │ ├── c_3d.jpg │ │ ├── errEst3D.m │ │ ├── reconstruction.m │ │ └── recording.m │ └── temp │ │ ├── Lim_duke_0066D_11287.pdf │ │ ├── Optical imaging and spectroscopy-Wiley.pdf │ │ ├── article_1327_Simulation_Codes │ │ ├── Code001 │ │ │ ├── Functions │ │ │ │ ├── E.tif │ │ │ │ ├── MyAdjointOperatorPropagation.m │ │ │ │ ├── MyAdjointPropagation.m │ │ │ │ ├── MyC2V.m │ │ │ │ ├── MyDiv3D.m │ │ │ │ ├── MyFieldsPropagation.m │ │ │ │ ├── MyForwardOperatorPropagation.m │ │ │ │ ├── MyForwardPropagation.m │ │ │ │ ├── MyMakingPhase.m │ │ │ │ ├── MyMakingPhase3D.m │ │ │ │ ├── MyProjectionTV.m │ │ │ │ ├── MyTV3D_conv.m │ │ │ │ ├── MyTVnorm.m │ │ │ │ ├── MyTVphi.m │ │ │ │ ├── MyTVpsi.m │ │ │ │ ├── MyV2C.m │ │ │ │ ├── N.tif │ │ │ │ ├── S.tif │ │ │ │ ├── TwIST.m │ │ │ │ ├── U.tif │ │ │ │ ├── plotdatacube.m │ │ │ │ ├── plotdatacubeTiff.asv │ │ │ │ └── plotdatacubeTiff.m │ │ │ └── mainHoloTomo.m │ │ ├── Code002 │ │ │ ├── MyFunctions │ │ │ │ ├── MyAdjointOperatorPropagation.m │ │ │ │ ├── MyAdjointOperatorPropagationMultiWaves.m │ │ │ │ ├── MyAdjointPropagation.m │ │ │ │ ├── MyC2V.m │ │ │ │ ├── MyCombinedPinvQ4DeblurringImageSpace.m │ │ │ │ ├── MyDerivationTV2D.m │ │ │ │ ├── MyDiv3D.m │ │ │ │ ├── MyFieldsPropagation.m │ │ │ │ ├── MyFieldsPropagationMultiWaves.m │ │ │ │ ├── MyForwardOperatorPropagation.m │ │ │ │ ├── MyForwardOperatorPropagationMultiWaves.m │ │ │ │ ├── MyForwardPropagation.m │ │ │ │ ├── MyFunc4DeblurringImageSpace.m │ │ │ │ ├── MyMakingPhase.m │ │ │ │ ├── MyMakingPhase3D.m │ │ │ │ ├── MyMakingPhase3DMultiWaves.m │ │ │ │ ├── MyPinvQ4DeblurringImageSpace.m │ │ │ │ ├── MyProjectionTV.m │ │ │ │ ├── MyQ4DeblurringImageSpace.m │ │ │ │ ├── MyQ4DeblurringImageSpaceMultiAngles.m │ │ │ │ ├── MyTV3D_conv.m │ │ │ │ ├── MyTVnorm.m │ │ │ │ ├── MyTVphi.m │ │ │ │ ├── MyTVpsi.m │ │ │ │ ├── MyTwIST.m │ │ │ │ ├── MyV2C.m │ │ │ │ ├── plotdatacube.m │ │ │ │ └── plotdatacubeTiff.m │ │ │ └── mainDiffuseTomo.m │ │ ├── Code003 │ │ │ ├── Functions │ │ │ │ ├── FresnelScalingAngularSpectrumBack.m │ │ │ │ ├── FresnelScalingAngularSpectrumFor.m │ │ │ │ ├── MyAdjointOperatorPropagation.m │ │ │ │ ├── MyAdjointPropagation.m │ │ │ │ ├── MyC2V.m │ │ │ │ ├── MyDiv3D.m │ │ │ │ ├── MyFieldsPropagation.m │ │ │ │ ├── MyForwardOperatorPropagation.m │ │ │ │ ├── MyForwardPropagation.m │ │ │ │ ├── MyMakingPhase.m │ │ │ │ ├── MyMakingPhase3D.m │ │ │ │ ├── MyProjectionTV.m │ │ │ │ ├── MyTV3D_conv.m │ │ │ │ ├── MyTVnorm.m │ │ │ │ ├── MyTVphi.m │ │ │ │ ├── MyTVpsi.m │ │ │ │ ├── MyV2C.m │ │ │ │ ├── TwIST.m │ │ │ │ └── plotdatacube.m │ │ │ └── mainSparseCoh.m │ │ └── Code004 │ │ │ ├── MyFunctions │ │ │ ├── FresnelScalingAngularSpectrumBack.m │ │ │ ├── FresnelScalingAngularSpectrumFor.m │ │ │ ├── MyAdjointOperatorPropagation.m │ │ │ ├── MyAdjointOperatorPropagationMultiWaves.m │ │ │ ├── MyAdjointPropagation.m │ │ │ ├── MyC2V.m │ │ │ ├── MyCombinedPinvQ4DeblurringImageSpace.m │ │ │ ├── MyDiv3D.m │ │ │ ├── MyFastFunc4DeblurringImageSpace.m │ │ │ ├── MyFieldsPropagation.m │ │ │ ├── MyFieldsPropagationMultiWaves.m │ │ │ ├── MyForwardOperatorPropagation.m │ │ │ ├── MyForwardOperatorPropagationMultiWaves.m │ │ │ ├── MyForwardPropagation.m │ │ │ ├── MyFunc4DeblurringImageSpace.m │ │ │ ├── MyMakingPhase.m │ │ │ ├── MyMakingPhase3D.m │ │ │ ├── MyMakingPhase3DMultiWaves.m │ │ │ ├── MyPinvQ4DeblurringImageSpace.m │ │ │ ├── MyProjectionTV.m │ │ │ ├── MyQ4DeblurringImageSpace.m │ │ │ ├── MyTV3D_conv.m │ │ │ ├── MyTVnorm.m │ │ │ ├── MyTVphi.m │ │ │ ├── MyTVpsi.m │ │ │ ├── MyTwIST.m │ │ │ ├── MyV2C.m │ │ │ ├── plotdatacube.m │ │ │ └── plotdatacubeTiff.m │ │ │ └── mainSparseIncoh.m │ │ ├── josaa-26-2-252.pdf │ │ └── oe-17-15-13040.pdf ├── result_analysis.m └── volObjGen.m └── docs ├── Gemfile ├── Gemfile.lock ├── _config.yml ├── _site ├── assets │ ├── css │ │ └── style.css │ ├── 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