├── 08062019_matlabbraggdiskdetection_withpowerlawfit.mat ├── 08072019_masking_results ├── convolution_kernel_radius_5.fig ├── convolution_kernel_radius_5.png ├── cross_correlation_peaks_before_any_smoothing.fig ├── cross_correlation_peaks_before_any_smoothing.png ├── disk_on_log_correlationmap_before_thresholding.fig ├── disk_on_log_correlationmap_before_thresholding.png ├── disk_on_log_correlationmap_overlay.fig ├── disk_on_log_correlationmap_overlay.png ├── disk_on_raw_data_overlay.fig ├── disk_on_raw_data_overlay.png ├── double_annulus_mask.fig ├── double_annulus_mask.png ├── double_annulus_peaks.fig ├── double_annulus_peaks.png ├── powerlaw_baseline_from_manualfit.fig ├── powerlaw_baseline_from_manualfit.png ├── powerlaw_baseline_without_center_removal.fig ├── powerlaw_baseline_without_center_removal.png ├── powerlaw_baselined_data.fig ├── powerlaw_baselined_data.png ├── radial_powerlw_fit.fig ├── radial_powerlw_fit.png ├── regular_hexagon_mask_structure.fig ├── regular_hexagon_mask_structure.png ├── uint8_DP_representation.fig ├── uint8_DP_representation.png ├── user_generated_mask_by_clicking.fig └── user_generated_mask_by_clicking.png ├── 08102019PoissonMLEBootstrapData.mat ├── 08112019_grapheneCOM_PoissonMLE_comparison.mat ├── 08142019strain_map_before_subpixel.mat ├── 08272019testingCutROI.mat ├── 09032019_first_DP_save_interference_tracking.mat ├── 09032019_intereference_pattern_tracking_ROIcut.mat ├── Beamspot_Visualization.fig ├── Beamspot_Visualization.png ├── BeamwidthTesting ├── beamwidth_testing.m └── beamwidth_testing2.m ├── CodeFromColin_NPKmods ├── .DS_Store ├── StrainDenoising │ ├── .DS_Store │ ├── Original │ │ ├── TGV.m │ │ ├── strainCalc01.m │ │ ├── strainCalc02.m │ │ └── strainCalc03.m │ ├── TGV_NPK.m │ ├── principle_strains_E1_absolute_range_-5.0e-02_5.0e-02.png │ ├── principle_strains_E2_absolute_range_-1.2e-01_0.png │ ├── principle_strains_combined.png │ ├── strain 70 plus 000 degrees ref.jpg │ ├── strain 70 plus 030 degrees ref.jpg │ ├── strain 70 plus 060 degrees ref.jpg │ ├── strain 70 plus 090 degrees ref.jpg │ ├── strain 70 plus 120 degrees ref.jpg │ ├── strain 70 plus 150 degrees ref.jpg │ ├── strainCalc01NPK.m │ ├── strainCalc02NPK.m │ ├── strainCalc03NPK.m │ └── theta_absolute_range_0_1.png └── StrainFitting │ ├── Gfitting.m │ ├── Gstrain01.m │ ├── Gstrain02.m │ ├── Gstrain03.m │ ├── Gstrain04NPKmod.m │ ├── Gstrain06.m │ ├── Gstrain07.m │ ├── Gstrain08.m │ ├── filtXray.m │ ├── makeFourierCoords.m │ ├── progressbar.m │ └── violetFire.m ├── DSC_BlinkingFit_Code ├── .DS_Store ├── 12202019FittingFunctions.mat ├── 12202019multislice_disk_centers.mat ├── 5_50x50_ss=1nm_C2=40um_alpha=1mrad_spot7_200ms_CL=130 bin=4_60kV__integration_disks.mat ├── 7_40x40_ss=0p5nm_C2=40um_alpha=1mrad_spot9_1s_CL=130 bin=2_scan90_60kV_NPKNormalized_andcropped__integration_disks.mat ├── 7_80x80_ss=2nm_C2=40um_alpha=1mrad_spot7_200ms_CL=130 bin=4_60kV_NPKnormalized__integration_disks.mat ├── 8_40x40_ss=0p5nm_C2=40um_alpha=1mrad_spot9_1s_CL=130 bin=2_scan0_60kV_NPK_Normalized_and_Cropped__integration_disks.mat ├── BilayerGraphene.m ├── Diffraction SI crop 20x20__integration_disks.mat ├── Diffraction SI crop__integration_disks.mat ├── FourDSTEM_Analysis_Engine.m ├── HamishTrigFittingFunction.m ├── HamishTrigFittingFunctionResidualsWrapper.m ├── MLE_testing.m ├── MLE_testing_2.m ├── PRISMmultisliceNPK_ExternalControl.m ├── SPscore.m ├── TEAM1DS7DiffractionSI__integration_disks.mat ├── TEAM1Day1Dataset4DiffractionSI__integration_disks.mat ├── TEAM1Day1Dataset7DiffractionSIcropped__integration_disks.mat ├── TranslatedBilayerGraphene.m ├── TwistedBilayerGraphene.m ├── blackorangecolormap.m ├── blackredcolormap.m ├── blacksilvercolormap.m ├── blackyellowcolormap.m ├── blinkingFittingFunction.m ├── blinkingfit_0123_dataset5.m ├── blinkingfit_0123_dataset6.m ├── blinkingfit_0123_dataset7.m ├── blinkingfit_0123_dataset7_RSbin2.m ├── blinkingfit_0123_dataset7_RSbin2_allouter.m ├── blinkingfit_0123_dataset7_RSbin4.m ├── blinkingfit_0123_dataset7_RSbin8.m ├── blinkingfit_1220_dataset3.m ├── blinkingfit_1220_dataset4.m ├── blinkingfit_1220_dataset7.m ├── blinkingfit_1220_dataset8.m ├── blinkingfit_1220_dataset9.m ├── centerAverages.m ├── circularGaussianPredfun2.m ├── circularGaussianResidfun2.m ├── curvefit_dataset17_toDSC.m ├── curvefit_dataset1_toDSC.m ├── curvefit_simulation_toDSC.m ├── curvefit_simulation_toDSC_trigfunction.m ├── custom_displacement_color_testing_script.m ├── diophantine.m ├── ds9disks.mat ├── extendedTrigFittingFunctionsResidualsWrapper.m ├── extendedZoneDisp2ReducedZoneDisp.m ├── find_DSC_blinking_functional_form.m ├── find_DSC_blinking_functional_form2.m ├── fire.m ├── gaussRotateLattice02.m ├── getCustomDisplacementColor.m ├── getDSCBasisVectors.m ├── getDSCHexagonRaster.m ├── getFullRadialElasticFit.m ├── getFullRadialElasticFit_lsqnonlin.m ├── getFullRadialElasticPred.m ├── getFullRadialLorentzianFit.m ├── getFullRadialLorentzianPred.m ├── getFullRadialPsuedoVoigtFit.m ├── getFullRadialPsuedoVoigtPred.m ├── getLatticePlaneNormalVectors.m ├── getTriangleColorLegend.m ├── hexagonMod.m ├── impointCallback.m ├── initial_driver.m ├── lsqnonlin_outfun.m ├── makeBlinkingPlot.m ├── makeConcentricRings.m ├── makeDataBlinkingPlot.m ├── makeDiskCenters.m ├── makeMultiDataBlinkingPlot.m ├── makeProjectedBlinkingPlot.m ├── make_DSC_curvefit_simulation_reference_plots.m ├── make_explanatory_DSC_plots.m ├── make_fitting_functions.m ├── medfilt2_circle.m ├── moireFitFun.m ├── moireFitFun2.m ├── moireFitFun3.m ├── moirePredFun3.m ├── movmeanfilt2_circle.m ├── multistartDiskOptimization.m ├── mygxy.fig ├── optimal_semiangle_calculation.m ├── plotDisplacementFields.m ├── predict_blinking_from_trig.m ├── project.m ├── project2.m ├── project2b.m ├── roiBoilerplate.m ├── simpleShearObjFcn.m ├── simpleShearPredfun.m ├── testTrigFittingFunction.m ├── trblg_driver.m ├── trblg_linesearch_driver.m ├── trblg_linesearch_driver2.m ├── trblg_raster_driver.m ├── triangulationColormap.m ├── trigFittingFunction2.m ├── trigFittingFunction2outer.m ├── trigFittingFunction_testing_script.m ├── trigFittingFunctions.m ├── trimArray.m ├── uniaxialStrainPredFun.m ├── uniaxialStrainPredFun2.m ├── validateBlinkingFittingFunction.m ├── vectorLine.m └── whiteburgundycolormap.m ├── Dependencies ├── .DS_Store ├── Colormaps │ ├── .DS_Store │ ├── README.txt │ ├── Thumbs.db │ ├── demo1.m │ ├── demo1_output.png │ ├── demo2.m │ ├── fake_parula.m │ ├── inferno.m │ ├── license.txt │ ├── magma.asv │ ├── magma.m │ ├── plasma.asv │ ├── plasma.m │ └── viridis.m ├── DivergingColormap │ ├── .DS_Store │ └── JonKing93-scaleColorMap-23ed82e │ │ ├── .DS_Store │ │ ├── Demo │ │ ├── demo_T_anomaly_data.mat │ │ ├── demo_colormap.mat │ │ └── demo_scaleColorMap.m │ │ ├── LICENSE.txt │ │ └── scaleColorMap.m ├── Export_fig │ ├── .gitignore │ ├── Export_fig.prj │ ├── ImageSelection.class │ ├── ImageSelection.java │ ├── LICENSE │ ├── README.md │ ├── append_pdfs.m │ ├── copyfig.m │ ├── crop_borders.m │ ├── eps2pdf.m │ ├── export_fig.m │ ├── fix_lines.m │ ├── ghostscript.m │ ├── hyperlink.m │ ├── im2gif.m │ ├── isolate_axes.m │ ├── pdf2eps.m │ ├── pdftops.m │ ├── print2array.m │ ├── print2eps.m │ ├── read_write_entire_textfile.m │ ├── resources │ │ └── project │ │ │ ├── Extensions.type.Root │ │ │ └── DependencyAnalysis.type.Extension │ │ │ │ └── ExternalFiles.type.Extension.xml │ │ │ ├── Project.xml │ │ │ ├── ProjectData.type.Info.xml │ │ │ ├── Root.type.Categories │ │ │ ├── FileClassCategory.type.Category.xml │ │ │ └── FileClassCategory.type.Category │ │ │ │ ├── artifact.type.Label.xml │ │ │ │ ├── convenience.type.Label.xml │ │ │ │ ├── derived.type.Label.xml │ │ │ │ ├── design.type.Label.xml │ │ │ │ ├── none.type.Label.xml │ │ │ │ ├── other.type.Label.xml │ │ │ │ └── test.type.Label.xml │ │ │ ├── Root.type.Files │ │ │ ├── .gitignore.type.File.xml │ │ │ ├── ImageSelection.class.type.File.xml │ │ │ ├── ImageSelection.java.type.File.xml │ │ │ ├── LICENSE.type.File.xml │ │ │ ├── README.md.type.File.xml │ │ │ ├── append_pdfs.m.type.File.xml │ │ │ ├── copyfig.m.type.File.xml │ │ │ ├── crop_borders.m.type.File.xml │ │ │ ├── eps2pdf.m.type.File.xml │ │ │ ├── export_fig.m.type.File.xml │ │ │ ├── fix_lines.m.type.File.xml │ │ │ ├── ghostscript.m.type.File.xml │ │ │ ├── im2gif.m.type.File.xml │ │ │ ├── isolate_axes.m.type.File.xml │ │ │ ├── pdf2eps.m.type.File.xml │ │ │ ├── pdftops.m.type.File.xml │ │ │ ├── print2array.m.type.File.xml │ │ │ ├── print2eps.m.type.File.xml │ │ │ ├── read_write_entire_textfile.m.type.File.xml │ │ │ ├── user_string.m.type.File.xml │ │ │ └── using_hg2.m.type.File.xml │ │ │ ├── Root.type.ProjectPath │ │ │ └── a533e478-c90b-4a1f-a45b-f8877af57bee.type.Reference.xml │ │ │ └── uuid-cc21a9b0-026d-4b70-9821-3eb23d2abf81.xml │ ├── user_string.m │ └── using_hg2.m ├── L1Magic │ ├── .DS_Store │ ├── TVM_image_denoise.m │ ├── l1magic.pdf │ └── l1magic │ │ ├── .DS_Store │ │ ├── Data │ │ ├── .DS_Store │ │ ├── RandomStates.mat │ │ ├── boats.mat │ │ └── camera.mat │ │ ├── Measurements │ │ ├── .DS_Store │ │ ├── A_f.m │ │ ├── A_fhp.m │ │ ├── At_f.m │ │ ├── At_fhp.m │ │ └── LineMask.m │ │ ├── Notes │ │ ├── .DS_Store │ │ ├── Figs │ │ │ ├── CVS │ │ │ │ ├── Entries │ │ │ │ ├── Repository │ │ │ │ └── Root │ │ │ ├── l1eqexample_minl2.eps │ │ │ ├── l1eqexample_minl2.pdf │ │ │ ├── l1eqexample_recovered.eps │ │ │ ├── l1eqexample_recovered.pdf │ │ │ ├── l1eqexample_signal.eps │ │ │ ├── l1eqexample_signal.pdf │ │ │ ├── phantom_backproj.eps │ │ │ ├── phantom_backproj.pdf │ │ │ ├── phantom_orig.eps │ │ │ ├── phantom_orig.pdf │ │ │ ├── phantom_sampling.eps │ │ │ ├── phantom_sampling.pdf │ │ │ ├── phantom_tv.eps │ │ │ └── phantom_tv.pdf │ │ ├── l1magic.bib │ │ ├── l1magic_notes.aux │ │ ├── l1magic_notes.bbl │ │ ├── l1magic_notes.blg │ │ ├── l1magic_notes.log │ │ ├── l1magic_notes.pdf │ │ └── l1magic_notes.tex │ │ ├── Optimization │ │ ├── .DS_Store │ │ ├── cgsolve.m │ │ ├── l1dantzig_pd.m │ │ ├── l1decode_pd.m │ │ ├── l1eq_pd.m │ │ ├── l1qc_logbarrier.m │ │ ├── l1qc_newton.m │ │ ├── tvdantzig_logbarrier.m │ │ ├── tvdantzig_newton.m │ │ ├── tveq_logbarrier.m │ │ ├── tveq_newton.m │ │ ├── tvqc_logbarrier.m │ │ └── tvqc_newton.m │ │ ├── README │ │ ├── l1dantzig_example.m │ │ ├── l1decode_example.m │ │ ├── l1eq_example.m │ │ ├── l1qc_example.m │ │ ├── tvdantzig_example.m │ │ ├── tveq_example.m │ │ ├── tveq_phantom_example.m │ │ ├── tvqc_example.m │ │ └── tvqc_quantization_example.m ├── MyColormaps │ ├── Pablomap1.png │ ├── Pablomap2.png │ ├── Pablomaps.png │ ├── makeColorMapFromImage.m │ ├── whiteburgundy.png │ └── whiteburgundyzoom.png ├── PSwarmM_v2_1 │ ├── .DS_Store │ ├── CheckStoppingCriteria.m │ ├── InitCache.m │ ├── InitPatternSearch.m │ ├── InitPopulation.m │ ├── PSwarm.m │ ├── ParticleSwarm.m │ ├── PenaltyEval.m │ ├── PollStep.m │ ├── Projection.m │ ├── QuadObjFun.m │ ├── Quad_MFN.m │ ├── RBF.m │ ├── RBFObjFun.m │ ├── README.txt │ ├── RunMOPSwarm.m │ ├── RunPSwarm.m │ ├── RunPSwarm_wild.m │ ├── Solve_all_bound_cons.m │ ├── Solve_all_lin_cons.m │ ├── UpdateInfo.m │ ├── ampl_obj.m │ ├── amplfunc.dll │ ├── hs024.m │ ├── hs024_obj.m │ ├── lgpl.txt │ ├── matampl.dll │ ├── matampl.mexw32 │ ├── models │ │ ├── Ji1.mod │ │ ├── Ji1.nl │ │ ├── Ji2.mod │ │ ├── Ji2.nl │ │ ├── Ji3.mod │ │ ├── Ji3.nl │ │ ├── Michalewicz1.mod │ │ ├── Michalewicz1.nl │ │ ├── Pinter_10_5_2.nl │ │ ├── Pinter_15_10_5.nl │ │ ├── Pinter_20_15_7.nl │ │ ├── Pinter_25_20_10.nl │ │ ├── Pinter_30_25_12.nl │ │ ├── Pinter_35_30_15.nl │ │ ├── Pinter_3_2_1.nl │ │ ├── Pinter_40_35_17.nl │ │ ├── Pinter_45_40_20.nl │ │ ├── Pinter_50_45_22.nl │ │ ├── Pinter_n_m.dat │ │ ├── Pinter_n_m.mod │ │ ├── ack.nl │ │ ├── antenna2.mod │ │ ├── antenna2.nl │ │ ├── ap.nl │ │ ├── avgasa.mod │ │ ├── avgasa.nl │ │ ├── avgasb.mod │ │ ├── avgasb.nl │ │ ├── bc4.mod │ │ ├── bc4.nl │ │ ├── bf1.nl │ │ ├── bf2.nl │ │ ├── bhs.nl │ │ ├── biggsc4.mod │ │ ├── biggsc4.nl │ │ ├── bl.nl │ │ ├── bp.nl │ │ ├── bunnag1.mod │ │ ├── bunnag1.nl │ │ ├── bunnag10.mod │ │ ├── bunnag10.nl │ │ ├── bunnag11.mod │ │ ├── bunnag11.nl │ │ ├── bunnag12.mod │ │ ├── bunnag12.nl │ │ ├── bunnag13.mod │ │ ├── bunnag13.nl │ │ ├── bunnag2.mod │ │ ├── bunnag2.nl │ │ ├── bunnag3.mod │ │ ├── bunnag3.nl │ │ ├── bunnag4.mod │ │ ├── bunnag4.nl │ │ ├── bunnag5.mod │ │ ├── bunnag5.nl │ │ ├── bunnag6.mod │ │ ├── bunnag6.nl │ │ ├── bunnag7.mod │ │ ├── bunnag7.nl │ │ ├── bunnag8.mod │ │ ├── bunnag8.nl │ │ ├── bunnag9.mod │ │ ├── bunnag9.nl │ │ ├── cb3.nl │ │ ├── cb6.nl │ │ ├── cm2.nl │ │ ├── cm4.nl │ │ ├── da.nl │ │ ├── dea.mod │ │ ├── dea.nl │ │ ├── em_10.nl │ │ ├── em_5.nl │ │ ├── ep.nl │ │ ├── ex2_1_1.mod │ │ ├── ex2_1_1.nl │ │ ├── ex2_1_10.mod │ │ ├── ex2_1_10.nl │ │ ├── ex2_1_2.mod │ │ ├── ex2_1_2.nl │ │ ├── ex2_1_3.mod │ │ ├── ex2_1_3.nl │ │ ├── ex2_1_4.mod │ │ ├── ex2_1_4.nl │ │ ├── ex2_1_5.mod │ │ ├── ex2_1_5.nl │ │ ├── ex2_1_6.mod │ │ ├── ex2_1_6.nl │ │ ├── ex2_1_7.mod │ │ ├── ex2_1_7.nl │ │ ├── exp.nl │ │ ├── expfita.mod │ │ ├── expfita.nl │ │ ├── expfitb.mod │ │ ├── expfitb.nl │ │ ├── expfitc.mod │ │ ├── expfitc.nl │ │ ├── fir_linear.mod │ │ ├── fir_linear.nl │ │ ├── fls.nl │ │ ├── fr.nl │ │ ├── fx_10.nl │ │ ├── fx_5.nl │ │ ├── g01.mod │ │ ├── g01.nl │ │ ├── genocop07.mod │ │ ├── genocop07.nl │ │ ├── genocop09.mod │ │ ├── genocop09.nl │ │ ├── genocop10.mod │ │ ├── genocop10.nl │ │ ├── genocop11.mod │ │ ├── genocop11.nl │ │ ├── goffin.mod │ │ ├── goffin.nl │ │ ├── gp.nl │ │ ├── grp.nl │ │ ├── gtm.mod │ │ ├── gtm.nl │ │ ├── gw.nl │ │ ├── h3.nl │ │ ├── h6.nl │ │ ├── hatfldh.mod │ │ ├── hatfldh.nl │ │ ├── himmelbi.mod │ │ ├── himmelbi.nl │ │ ├── hm.nl │ │ ├── hm1.nl │ │ ├── hm2.nl │ │ ├── hm3.nl │ │ ├── hm4.nl │ │ ├── hm5.nl │ │ ├── hs021.mod │ │ ├── hs021.nl │ │ ├── hs024.mod │ │ ├── hs024.nl │ │ ├── hs035.mod │ │ ├── hs035.nl │ │ ├── hs036.mod │ │ ├── hs036.nl │ │ ├── hs037.mod │ │ ├── hs037.nl │ │ ├── hs044.mod │ │ ├── hs044.nl │ │ ├── hs076.mod │ │ ├── hs076.nl │ │ ├── hs086.mod │ │ ├── hs086.nl │ │ ├── hs118.mod │ │ ├── hs118.nl │ │ ├── hs21mod.mod │ │ ├── hs21mod.nl │ │ ├── hs268.mod │ │ ├── hs268.nl │ │ ├── hs35mod.mod │ │ ├── hs35mod.nl │ │ ├── hs44new.mod │ │ ├── hs44new.nl │ │ ├── hsk.nl │ │ ├── hubfit.mod │ │ ├── hubfit.nl │ │ ├── hv.nl │ │ ├── ir0.nl │ │ ├── ir1.nl │ │ ├── ir2.nl │ │ ├── ir3.nl │ │ ├── ir4.nl │ │ ├── ir5.nl │ │ ├── kl.nl │ │ ├── ks.nl │ │ ├── ksip.mod │ │ ├── ksip.nl │ │ ├── liswet1.mod │ │ ├── liswet1.nl │ │ ├── liswet10.mod │ │ ├── liswet10.nl │ │ ├── liswet11.mod │ │ ├── liswet11.nl │ │ ├── liswet12.mod │ │ ├── liswet12.nl │ │ ├── liswet2.mod │ │ ├── liswet2.nl │ │ ├── liswet3.mod │ │ ├── liswet3.nl │ │ ├── liswet4.mod │ │ ├── liswet4.nl │ │ ├── liswet5.mod │ │ ├── liswet5.nl │ │ ├── liswet6.mod │ │ ├── liswet6.nl │ │ ├── liswet7.mod │ │ ├── liswet7.nl │ │ ├── liswet8.mod │ │ ├── liswet8.nl │ │ ├── liswet9.mod │ │ ├── liswet9.nl │ │ ├── lj1_38.nl │ │ ├── lj1_75.nl │ │ ├── lj1_98.nl │ │ ├── lj2_38.nl │ │ ├── lj2_75.nl │ │ ├── lj2_98.nl │ │ ├── lj3_38.nl │ │ ├── lj3_75.nl │ │ ├── lj3_98.nl │ │ ├── lm1.nl │ │ ├── lm2_10.nl │ │ ├── lm2_5.nl │ │ ├── lms1a.nl │ │ ├── lms1b.nl │ │ ├── lms2.nl │ │ ├── lms3.nl │ │ ├── lms5.nl │ │ ├── lowpass.mod │ │ ├── lowpass.nl │ │ ├── lsqfit.mod │ │ ├── lsqfit.nl │ │ ├── lv8.nl │ │ ├── makela4.mod │ │ ├── makela4.nl │ │ ├── mc.nl │ │ ├── mcp.nl │ │ ├── mgp.nl │ │ ├── mgw_10.nl │ │ ├── mgw_2.nl │ │ ├── mgw_20.nl │ │ ├── ml_10.nl │ │ ├── ml_5.nl │ │ ├── mosarqp1.mod │ │ ├── mosarqp1.nl │ │ ├── mosarqp2.mod │ │ ├── mosarqp2.nl │ │ ├── mr.nl │ │ ├── mrp.nl │ │ ├── ms1.nl │ │ ├── ms2.nl │ │ ├── nf2.nl │ │ ├── nf3_10.nl │ │ ├── nf3_15.nl │ │ ├── nf3_20.nl │ │ ├── nf3_25.nl │ │ ├── nf3_30.nl │ │ ├── nuffield_continuum.mod │ │ ├── nuffield_continuum.nl │ │ ├── oet1.mod │ │ ├── oet1.nl │ │ ├── oet3.mod │ │ ├── oet3.nl │ │ ├── osp_10.nl │ │ ├── osp_20.nl │ │ ├── pentagon.mod │ │ ├── pentagon.nl │ │ ├── plj_38.nl │ │ ├── plj_75.nl │ │ ├── plj_98.nl │ │ ├── powell20.mod │ │ ├── powell20.nl │ │ ├── pp.nl │ │ ├── prd.nl │ │ ├── pt.mod │ │ ├── pt.nl │ │ ├── ptm.nl │ │ ├── pwq.nl │ │ ├── rb.nl │ │ ├── rg_10.nl │ │ ├── rg_2.nl │ │ ├── s10.nl │ │ ├── s224.mod │ │ ├── s224.nl │ │ ├── s231.mod │ │ ├── s231.nl │ │ ├── s232.mod │ │ ├── s232.nl │ │ ├── s250.mod │ │ ├── s250.nl │ │ ├── s251.mod │ │ ├── s251.nl │ │ ├── s253.mod │ │ ├── s253.nl │ │ ├── s268.mod │ │ ├── s268.nl │ │ ├── s277.mod │ │ ├── s277.nl │ │ ├── s278.mod │ │ ├── s278.nl │ │ ├── s279.mod │ │ ├── s279.nl │ │ ├── s280.mod │ │ ├── s280.nl │ │ ├── s331.mod │ │ ├── s331.nl │ │ ├── s340.mod │ │ ├── s340.nl │ │ ├── s354.mod │ │ ├── s354.nl │ │ ├── s359.mod │ │ ├── s359.nl │ │ ├── s392.mod │ │ ├── s392.nl │ │ ├── s5.nl │ │ ├── s7.nl │ │ ├── sal_10.nl │ │ ├── sal_5.nl │ │ ├── sbt.nl │ │ ├── sf1.nl │ │ ├── sf2.nl │ │ ├── shv1.nl │ │ ├── shv2.nl │ │ ├── simpllpa.mod │ │ ├── simpllpa.nl │ │ ├── simpllpb.mod │ │ ├── simpllpb.nl │ │ ├── sin_10.nl │ │ ├── sin_20.nl │ │ ├── sipow1.mod │ │ ├── sipow1.nl │ │ ├── sipow1m.mod │ │ ├── sipow1m.nl │ │ ├── sipow2.mod │ │ ├── sipow2.nl │ │ ├── sipow2m.mod │ │ ├── sipow2m.nl │ │ ├── sipow3.mod │ │ ├── sipow3.nl │ │ ├── sipow4.mod │ │ ├── sipow4.nl │ │ ├── st_17.nl │ │ ├── st_9.nl │ │ ├── stancmin.mod │ │ ├── stancmin.nl │ │ ├── stg.nl │ │ ├── structure2.mod │ │ ├── structure2.nl │ │ ├── swf.nl │ │ ├── sz.nl │ │ ├── szzs.nl │ │ ├── tfi2.mod │ │ ├── tfi2.nl │ │ ├── vaz.nl │ │ ├── weapons.mod │ │ ├── weapons.nl │ │ ├── wf.nl │ │ ├── xor.nl │ │ ├── yao.mod │ │ ├── yao.nl │ │ ├── zecevic2.mod │ │ ├── zecevic2.nl │ │ ├── zkv_10.nl │ │ ├── zkv_2.nl │ │ ├── zkv_20.nl │ │ ├── zkv_5.nl │ │ ├── zlk1.nl │ │ ├── zlk2a.nl │ │ ├── zlk2b.nl │ │ ├── zlk3a.nl │ │ ├── zlk3b.nl │ │ ├── zlk3c.nl │ │ ├── zlk4.nl │ │ ├── zlk5.nl │ │ └── zzs.nl │ ├── mve_presolve.m │ ├── mve_solver.m │ └── outputfcn.m ├── ellipse │ ├── ellipse │ │ └── ellipse.m │ └── license.txt ├── fnnls.m └── phase_unwrap_TV_min_to_FileExchange │ ├── TV_min.m │ ├── denoised_unwrap.m │ ├── html │ └── phase_unwrap_TV_min.html │ ├── license.txt │ ├── phase_unwrap_TV_min.m │ └── phase_wrap.m ├── DisplacementVisualizations ├── .DS_Store ├── AtomPlot │ ├── .DS_Store │ ├── ZoomRegion_DS4S1atomdisplacement.png │ ├── make_atom_displacements_plot.m │ └── scatterSpherical.m └── DisplacementDensityPlot │ ├── Ksdensity_2D_contourf_coarse_uniformunits.fig │ ├── Ksdensity_2D_contourf_fine_uniformunits.fig │ ├── Ksdensity_3D_uniformunits.fig │ └── displacement_density_plot.m ├── Exiting function.ps ├── Filters ├── .DS_Store ├── RotationCalibratedTGVscripts │ ├── DS10S2_rotcalibrated_strainmaps.m │ ├── DS11S2_rotcalibrated_strainmaps.m │ ├── DS12S2_rotcalibrated_strainmaps.m │ ├── DS15S2_rotcalibrated_strainmaps.m │ ├── DS1S2_rotcalibrated_strainmaps.m │ ├── DS26S1_rotcalibrated_strainmaps.m │ ├── DS3S2_rotcalibrated_strainmaps.m │ ├── DS8S2_rotcalibrated_strainmaps.m │ └── DS9S2_rotcalibrated_strainmaps.m ├── TGVstrainmappingscripts │ ├── DS10_TGV_strainmaps.m │ ├── DS15_TGV_strainmaps.m │ ├── DS18_TGV_quant_strainmaps.m │ ├── DS18_TGV_strainmaps.m │ ├── DS18_TGVnodivide2_quant_strainmaps.m │ ├── DS18_TGVnodivide2_strainmaps.m │ ├── DS18_simplesheardecomp.m │ ├── DS1_TGV_strainmaps.m │ ├── DS26_TGV_strainmaps.m │ ├── DS2_TGV_strainmaps.m │ ├── DS2_TGVtuning_script.m │ ├── DS2_simplesheardecomp.m │ ├── DS30S2_TGV_strainmaps.m │ ├── DS3_TGV_strainmaps.m │ ├── DS3_TVG_within_sample_trends.m │ ├── DS4_TGV_nodivide2_strainmaps.m │ ├── DS4_TGV_strainmaps.m │ ├── DS5_TGV_strainmaps.m │ ├── DS6_TGV_strainmaps.m │ ├── DS6_TVG_within_sample_trends.m │ ├── DS8S2_TGV_strainmaps.m │ ├── DS8_TGV_nodivide2_strainmaps.m │ ├── DS8_TGV_strainmaps.m │ ├── DS9S2_TGV_strainmaps.m │ └── TGV_testing.m ├── TwistedBilayerGrapheneAugmented.m ├── buildFilterStruct.m ├── buildFilterStructPreset.m ├── filterDisplacement.m ├── filterMedianOutlier.m ├── filterStrain.m ├── filter_validation.m ├── gaussRotateLattice03.m └── heterostrain_atomic_simulator.m ├── FirstBeamspotCurves.fig ├── FirstBeamspotCurves.png ├── FitBoundRefactoring ├── DisplacementEquivalenceClass.m ├── DisplacementEquivalenceClassMagnet.m ├── PoissonFittingFunction.m ├── computeGradient.m ├── examine_third_ring.m ├── extendedMultistartDiskOptimization.m ├── extendedTrigFittingFunctions.m ├── followMinPath.m ├── getTopN.m ├── hotspot_hunting_DS4.m ├── hotspot_probability_calculation.m ├── interactive_blinking_script.m ├── plotLine.m ├── revise_distance_metric.m ├── shiftFittingBoundsMagnet.m └── strain_visualization_driver.m ├── GeometryStatistics ├── .DS_Store ├── AAFunctionInvestigation │ ├── DS2_AA_LineCut_06082020.fig │ └── DS2_AA_LineCut_06082020.png ├── AA_Gaussian_Circle_scripts │ ├── DS10S1_GaussianCircleFits.m │ ├── DS12S2_GaussianCircleFits.m │ ├── DS13S2_GaussianCircleFits.m │ ├── DS14S2_GaussianCircleFits.m │ ├── DS15S2_GaussianCircleFits.m │ ├── DS17S2_GaussianCircleFits.m │ ├── DS1S1_GaussianCircleFits.m │ ├── DS1S2_GaussianCircleFits.m │ ├── DS20S2_GaussianCircleFits.m │ ├── DS21S2_GaussianCircleFits.m │ ├── DS2S1_GaussianCircleFits.m │ ├── DS30S2_GaussianCircleFits.m │ ├── DS4S1_GaussianCircleFits.m │ ├── DS4S2_GaussianCircleFits.m │ ├── DS5S1_GaussianCircleFits.m │ ├── DS8S1_GaussianCircleFits.m │ └── makeAAradiusplot.m ├── ChiralFixedDataScripts05312020 │ ├── DS8_anglehistogram.fig │ ├── DS8_anglehistogram.png │ ├── register_geometry_DS10_chiralfixed.m │ ├── register_geometry_DS15_chiralfixed.m │ ├── register_geometry_DS18_chiralfixed.m │ ├── register_geometry_DS1_chiralfixed.m │ ├── register_geometry_DS22_chiralfixed.m │ ├── register_geometry_DS26_chiralfixed.m │ ├── register_geometry_DS26_chiralfixed_noprefactor.m │ ├── register_geometry_DS2_chiralfixed.m │ ├── register_geometry_DS4_chiralfixed.m │ ├── register_geometry_DS5_chiralfixed.m │ └── register_geometry_DS8_chiralfixed.m ├── DataScriptsApr12 │ ├── .DS_Store │ ├── register_SPgeometry_DS4_Apr12.m │ ├── register_geometry_DS10_05232020.m │ ├── register_geometry_DS10_Apr12.m │ ├── register_geometry_DS15.m │ ├── register_geometry_DS18.m │ ├── register_geometry_DS2.m │ ├── register_geometry_DS22.m │ ├── register_geometry_DS26_notApr12.m │ ├── register_geometry_DS26_trulyApr12.m │ ├── register_geometry_DS4_Apr12.m │ ├── register_geometry_DS5.m │ ├── register_geometry_DS7_notApr12.m │ ├── register_geometry_DS7_trulyApr12.m │ └── register_geometry_DS8.m ├── SPwidth │ ├── 07112020_SPwidth_figure_calculation2better.fig │ ├── 07112020_SPwidth_figure_calculation2better.png │ ├── DS10S1_SPwidth.fig │ ├── DS10S1_SPwidth.m │ ├── DS12S2_SPwidth.m │ ├── DS15S2_SPwidth.fig │ ├── DS15S2_SPwidth.m │ ├── DS26S1_SPwidth.m │ ├── DS2S1_SPwidth.fig │ ├── DS2S1_SPwidth.m │ ├── DS30S2_SPwidth.m │ ├── DS3S2_SPwidth.m │ ├── DS4S1_SPwidth.fig │ ├── DS4S1_SPwidth.m │ ├── DS5S1_SPwidth.fig │ ├── DS5S1_SPwidth.m │ ├── DS8S1.fig │ ├── DS8S2_SPwidth.fig │ ├── DS8S2_SPwidth.m │ ├── DS9S2_SPwidth.fig │ ├── DS9S2_SPwidth.m │ ├── SPwidth_figure.fig │ ├── SPwidth_figure.png │ ├── SPwidth_testing_script.m │ └── make_SPwidth_figure.m ├── Session2Scripts │ ├── DS2S2_GaussianCircleFits.m │ ├── register_geometry_DS10S2.m │ ├── register_geometry_DS11S2.m │ ├── register_geometry_DS12S2.m │ ├── register_geometry_DS15S2.m │ ├── register_geometry_DS1S2.m │ ├── register_geometry_DS23S2.m │ ├── register_geometry_DS24S2.m │ ├── register_geometry_DS25S2.m │ ├── register_geometry_DS26S2.m │ ├── register_geometry_DS30S2.m │ ├── register_geometry_DS3S2.m │ ├── register_geometry_DS4S2.m │ ├── register_geometry_DS8S2.m │ └── register_geometry_DS9S2.m ├── TearChiralFixedDataScripts06012020 │ ├── register_geometry_DS3_tearchiralfixed.m │ └── register_geometry_DS6_tearchiralfixed.m ├── UncertaintyQuantification │ ├── AAmask_linearfitfun.m │ ├── AAmask_linearpredfun.m │ ├── DS8_AAGaussianCircle_bootstrapping_driver.m │ ├── DS8_AAGaussianCircle_testing_driver.m │ ├── DS8_AAGaussianellipse_bootstrapping_driver.m │ ├── DS8_AAradius_bootstrapping_driver.m │ ├── Sigma0p1_1p37_heterostrainhistogram.fig │ ├── Sigma0p1_1p37_heterostrainhistogramdata.mat │ ├── Sigma0p1_1p37_heterostraintriangulation.png │ ├── Sigma0p1_1p37_moiretwistanglehistogram.fig │ ├── Sigma0p1_1p37data.mat │ ├── Sigma0p3_0p63moire_heterostrain_histogram.fig │ ├── Sigma0p3_0p63moire_heterostrainmap.fig │ ├── Sigma0p3_0p63moire_twistangle_histogram.fig │ ├── heterostrain_uncertainty.m │ ├── setFacetTwistAngles_refactored.m │ └── triangulation_uncertainty.m ├── anglefailure1.jpeg ├── bwneighborerode.m ├── bwshortestpath.m ├── critical_amplitude_Tadmor_test.m ├── ellipticGaussianPredfun.m ├── ellipticGaussianPredfun2.m ├── ellipticGaussianResidfun.m ├── ellipticGaussianResidfun2.m ├── fit_AA_to_ellipse.m ├── getFirstOrderConnectivityFilters.m ├── getjacobian.m ├── padArray.m ├── process_AB.m ├── registerSP.m ├── registerUniqueSPLines.m ├── savitzky_golay_filter_smooth_outline.m ├── triangulation_script.m └── wrongangle2.jpeg ├── MaddieStuff ├── .DS_Store ├── 04062020AnnealingStudiesForNPK │ ├── 04062020AnnealingSchedule1Results_lean.mat │ ├── 04062020AnnealingSchedule1Results_lean_test2.mat │ ├── 04062020AnnealingSchedule2Results_lean.mat │ ├── 04062020AnnealingSchedule3Results_lean.mat │ ├── 04062020AnnealingSchedule4Results_lean.mat │ ├── annealing_schedule_1.m │ ├── annealing_schedule_2.m │ ├── annealing_schedule_3.m │ └── annealing_schedule_4.m ├── Diffraction SI__integration_disks.mat ├── FourDSTEM_Analysis_Engine_MV02132020.m ├── MV_02262020_10__integration_disks.mat ├── MV_02262020_6__integration_disks.mat ├── MV_02262020_7__integration_disks.mat ├── Multislice │ └── example_multislice_driver.m ├── Script_for_data_fitting.m ├── bluewhitered.m ├── first_script_0209_for_simulations_and_pictures.m ├── redblue.m ├── revised2_script_for_data_fitting.m └── revised_script_for_data_fitting.m ├── NPKDataScripts ├── dataset10_polar_interpolation.m ├── dataset7_polar_interpolation.m └── ringed_Gaussian_testing_script.m ├── PoissonPowerlawBootfun.m ├── PositionFitCode ├── .DS_Store ├── 7_80x80_ss=1nm_C2=40um_alpha=1mrad_spot7_100ms_CL=130 bin=4_60kV__integration_disks.mat ├── 8_80x80_ss=1nm_C2=40um_alpha=1mrad_spot7_100ms_CL=130 bin=4_rot=90_60kV__integration_disks.mat ├── Diffraction SI crop 20x20__integration_disks.mat ├── Gstrain04NPKmod.m ├── TestingBNKernels │ ├── UnencouragingDiskPositions_DS8_0203.fig │ ├── innerrow_bottomrihgt_DS8_0203.fig │ └── outerrow_atverytop.fig ├── convolve2.zip ├── convolve2 │ ├── convolve2.m │ ├── exindex.m │ └── license.txt ├── makeDiskCentersForPositionFit.m ├── npkMedFilt2Displacement.m ├── positionfit_0203_DS7_testing.m ├── positionfit_0203_DS8_testing.m ├── positionfit_1023_DS1_testing.m └── positionfit_problemcrop_testing.m ├── Pseudostacking ├── .DS_Store ├── 01192021_SecondRevision │ ├── .DS_Store │ ├── DS1S1 │ │ ├── get_cropped_DS1S1_newps.m │ │ └── get_cropped_DS1S1_newps.m~ │ ├── FiguresToUse │ │ ├── .DS_Store │ │ ├── PseudostackingFive_DS_10_0p63deg.fig │ │ ├── PseudostackingFive_DS_18_0p14.fig │ │ ├── PseudostackingFive_DS_2_1p03.fig │ │ ├── PseudostackingFive_DS_8_1p37deg.fig │ │ ├── PseudostackingFive_criteria.fig │ │ ├── PseudostackingTrends_fivecategories.fig │ │ ├── PseudostackingTrends_fivecategories.png │ │ ├── WrongColors │ │ │ ├── FivePartitionCriterion.fig │ │ │ ├── FivePartitionCriterion.png │ │ │ ├── FivePartitionCriterion_zoomed.png │ │ │ ├── PseudostackingFive_DS_10_0p63deg.fig │ │ │ ├── PseudostackingFive_DS_10_0p63deg.png │ │ │ ├── PseudostackingFive_DS_18_0p14deg.fig │ │ │ ├── PseudostackingFive_DS_18_0p14deg.png │ │ │ ├── PseudostackingFive_DS_2_1p03deg.fig │ │ │ ├── PseudostackingFive_DS_2_1p03deg.png │ │ │ ├── PseudostackingFive_DS_8_1p37deg.fig │ │ │ └── PseudostackingFive_DS_8_1p37deg.png │ │ └── verify_fivecategory_pseudostacking_criterion.m │ ├── Pseudostacking_DS_10.fig │ ├── Pseudostacking_DS_10.png │ ├── Pseudostacking_DS_10S2.fig │ ├── Pseudostacking_DS_10S2.png │ ├── Pseudostacking_DS_11S2.fig │ ├── Pseudostacking_DS_11S2.png │ ├── Pseudostacking_DS_12S2.fig │ ├── Pseudostacking_DS_12S2.png │ ├── Pseudostacking_DS_15.fig │ ├── Pseudostacking_DS_15.png │ ├── Pseudostacking_DS_15S2.fig │ ├── Pseudostacking_DS_15S2.png │ ├── Pseudostacking_DS_18.fig │ ├── Pseudostacking_DS_18.png │ ├── Pseudostacking_DS_1S2.fig │ ├── Pseudostacking_DS_1S2.png │ ├── Pseudostacking_DS_2.fig │ ├── Pseudostacking_DS_2.png │ ├── Pseudostacking_DS_23S2.fig │ ├── Pseudostacking_DS_23S2.png │ ├── Pseudostacking_DS_24S2.fig │ ├── Pseudostacking_DS_24S2.png │ ├── Pseudostacking_DS_25S2.fig │ ├── Pseudostacking_DS_25S2.png │ ├── Pseudostacking_DS_26.fig │ ├── Pseudostacking_DS_26.png │ ├── Pseudostacking_DS_30S2.fig │ ├── Pseudostacking_DS_30S2.png │ ├── Pseudostacking_DS_3S2.fig │ ├── Pseudostacking_DS_3S2.png │ ├── Pseudostacking_DS_4.fig │ ├── Pseudostacking_DS_4.png │ ├── Pseudostacking_DS_5.fig │ ├── Pseudostacking_DS_5.png │ ├── Pseudostacking_DS_8.fig │ ├── Pseudostacking_DS_8.png │ ├── Pseudostacking_DS_8S2.fig │ ├── Pseudostacking_DS_8S2.png │ ├── Pseudostacking_DS_9S2.fig │ ├── Pseudostacking_DS_9S2.png │ ├── WrongColors │ │ ├── Pseudostacking_DS_10.fig │ │ ├── Pseudostacking_DS_10.png │ │ ├── Pseudostacking_DS_10S2.fig │ │ ├── Pseudostacking_DS_10S2.png │ │ ├── Pseudostacking_DS_11S2.fig │ │ ├── Pseudostacking_DS_11S2.png │ │ ├── Pseudostacking_DS_12S2.fig │ │ ├── Pseudostacking_DS_12S2.png │ │ ├── Pseudostacking_DS_15.fig │ │ ├── Pseudostacking_DS_15.png │ │ ├── Pseudostacking_DS_15S2.fig │ │ ├── Pseudostacking_DS_15S2.png │ │ ├── Pseudostacking_DS_18.fig │ │ ├── Pseudostacking_DS_18.png │ │ ├── Pseudostacking_DS_1S2.fig │ │ ├── Pseudostacking_DS_1S2.png │ │ ├── Pseudostacking_DS_2.fig │ │ ├── Pseudostacking_DS_2.png │ │ ├── Pseudostacking_DS_23S2.fig │ │ ├── Pseudostacking_DS_23S2.png │ │ ├── Pseudostacking_DS_24S2.fig │ │ ├── Pseudostacking_DS_24S2.png │ │ ├── Pseudostacking_DS_25S2.fig │ │ ├── Pseudostacking_DS_25S2.png │ │ ├── Pseudostacking_DS_26.fig │ │ ├── Pseudostacking_DS_26.png │ │ ├── Pseudostacking_DS_30S2.fig │ │ ├── Pseudostacking_DS_30S2.png │ │ ├── Pseudostacking_DS_3S2.fig │ │ ├── Pseudostacking_DS_3S2.png │ │ ├── Pseudostacking_DS_4.fig │ │ ├── Pseudostacking_DS_4.png │ │ ├── Pseudostacking_DS_5.fig │ │ ├── Pseudostacking_DS_5.png │ │ ├── Pseudostacking_DS_8.fig │ │ ├── Pseudostacking_DS_8.png │ │ ├── Pseudostacking_DS_8S2.fig │ │ ├── Pseudostacking_DS_8S2.png │ │ ├── Pseudostacking_DS_9S2.fig │ │ └── Pseudostacking_DS_9S2.png │ ├── dumpfolder │ │ ├── .DS_Store │ │ ├── Pseudostacking_DS_10.fig │ │ ├── Pseudostacking_DS_10.png │ │ ├── Pseudostacking_DS_10S2.fig │ │ ├── Pseudostacking_DS_10S2.png │ │ ├── Pseudostacking_DS_11S2.fig │ │ ├── Pseudostacking_DS_11S2.png │ │ ├── Pseudostacking_DS_12S2.fig │ │ ├── Pseudostacking_DS_12S2.png │ │ ├── Pseudostacking_DS_15.fig │ │ ├── Pseudostacking_DS_15.png │ │ ├── Pseudostacking_DS_15S2.fig │ │ ├── Pseudostacking_DS_15S2.png │ │ ├── Pseudostacking_DS_18.fig │ │ ├── Pseudostacking_DS_18.png │ │ ├── Pseudostacking_DS_1S2.fig │ │ ├── Pseudostacking_DS_1S2.png │ │ ├── Pseudostacking_DS_2.fig │ │ ├── Pseudostacking_DS_2.png │ │ ├── Pseudostacking_DS_23S2.fig │ │ ├── Pseudostacking_DS_23S2.png │ │ ├── Pseudostacking_DS_24S2.fig │ │ ├── Pseudostacking_DS_24S2.png │ │ ├── Pseudostacking_DS_25S2.fig │ │ ├── Pseudostacking_DS_25S2.png │ │ ├── Pseudostacking_DS_26.fig │ │ ├── Pseudostacking_DS_26.png │ │ ├── Pseudostacking_DS_30S2.fig │ │ ├── Pseudostacking_DS_30S2.png │ │ ├── Pseudostacking_DS_3S2.fig │ │ ├── Pseudostacking_DS_3S2.png │ │ ├── Pseudostacking_DS_4.fig │ │ ├── Pseudostacking_DS_4.png │ │ ├── Pseudostacking_DS_5.fig │ │ ├── Pseudostacking_DS_5.png │ │ ├── Pseudostacking_DS_8.fig │ │ ├── Pseudostacking_DS_8.png │ │ ├── Pseudostacking_DS_8S2.fig │ │ ├── Pseudostacking_DS_8S2.png │ │ ├── Pseudostacking_DS_9S2.fig │ │ └── Pseudostacking_DS_9S2.png │ └── five_category_pseudostacking.m ├── 07292020REvised │ ├── PS_fulldata.mat │ ├── Pseudostacking_DS_10.fig │ ├── Pseudostacking_DS_10.png │ ├── Pseudostacking_DS_10S2.fig │ ├── Pseudostacking_DS_10S2.png │ ├── Pseudostacking_DS_11S2.fig │ ├── Pseudostacking_DS_11S2.png │ ├── Pseudostacking_DS_12S2.fig │ ├── Pseudostacking_DS_12S2.png │ ├── Pseudostacking_DS_15.fig │ ├── Pseudostacking_DS_15.png │ ├── Pseudostacking_DS_15S2.fig │ ├── Pseudostacking_DS_15S2.png │ ├── Pseudostacking_DS_18.fig │ ├── Pseudostacking_DS_18.png │ ├── Pseudostacking_DS_1S2.fig │ ├── Pseudostacking_DS_1S2.png │ ├── Pseudostacking_DS_2.fig │ ├── Pseudostacking_DS_2.png │ ├── Pseudostacking_DS_23S2.fig │ ├── Pseudostacking_DS_23S2.png │ ├── Pseudostacking_DS_24S2.fig │ ├── Pseudostacking_DS_24S2.png │ ├── Pseudostacking_DS_25S2.fig │ ├── Pseudostacking_DS_25S2.png │ ├── Pseudostacking_DS_26.fig │ ├── Pseudostacking_DS_26.png │ ├── Pseudostacking_DS_30S2.fig │ ├── Pseudostacking_DS_30S2.png │ ├── Pseudostacking_DS_3S2.fig │ ├── Pseudostacking_DS_3S2.png │ ├── Pseudostacking_DS_4.fig │ ├── Pseudostacking_DS_4.png │ ├── Pseudostacking_DS_5.fig │ ├── Pseudostacking_DS_5.png │ ├── Pseudostacking_DS_8.fig │ ├── Pseudostacking_DS_8.png │ ├── Pseudostacking_DS_8S2.fig │ ├── Pseudostacking_DS_8S2.png │ ├── Pseudostacking_DS_9S2.fig │ ├── Pseudostacking_DS_9S2.png │ ├── Revist11082020 │ │ ├── Pseudostacking_DS_10.fig │ │ ├── Pseudostacking_DS_10.png │ │ ├── Pseudostacking_DS_10S2.fig │ │ ├── Pseudostacking_DS_10S2.png │ │ ├── Pseudostacking_DS_11S2.fig │ │ ├── Pseudostacking_DS_11S2.png │ │ ├── Pseudostacking_DS_12S2.fig │ │ ├── Pseudostacking_DS_12S2.png │ │ ├── Pseudostacking_DS_15.fig │ │ ├── Pseudostacking_DS_15.png │ │ ├── Pseudostacking_DS_15S2.fig │ │ ├── Pseudostacking_DS_15S2.png │ │ ├── Pseudostacking_DS_18.fig │ │ ├── Pseudostacking_DS_18.png │ │ ├── Pseudostacking_DS_1S2.fig │ │ ├── Pseudostacking_DS_1S2.png │ │ ├── Pseudostacking_DS_2.fig │ │ ├── Pseudostacking_DS_2.png │ │ ├── Pseudostacking_DS_23S2.fig │ │ ├── Pseudostacking_DS_23S2.png │ │ ├── Pseudostacking_DS_24S2.fig │ │ ├── Pseudostacking_DS_24S2.png │ │ ├── Pseudostacking_DS_25S2.fig │ │ ├── Pseudostacking_DS_25S2.png │ │ ├── Pseudostacking_DS_26.fig │ │ ├── Pseudostacking_DS_26.png │ │ ├── Pseudostacking_DS_30S2.fig │ │ ├── Pseudostacking_DS_30S2.png │ │ ├── Pseudostacking_DS_3S2.fig │ │ ├── Pseudostacking_DS_3S2.png │ │ ├── Pseudostacking_DS_4.fig │ │ ├── Pseudostacking_DS_4.png │ │ ├── Pseudostacking_DS_5.fig │ │ ├── Pseudostacking_DS_5.png │ │ ├── Pseudostacking_DS_8.fig │ │ ├── Pseudostacking_DS_8.png │ │ ├── Pseudostacking_DS_8S2.fig │ │ ├── Pseudostacking_DS_8S2.png │ │ ├── Pseudostacking_DS_9S2.fig │ │ └── Pseudostacking_DS_9S2.png │ ├── revised_pseudostacking.m │ ├── revised_pseudostacking_23.m │ └── revised_pseudostacking_23_25fixed_twoextra.m ├── get_expected_areas.m ├── get_pseudostacking_trends.m ├── get_pseudostacking_trends_newdatacrit_minimalTGV.m ├── get_pseudostacking_trends_nn_noTGVyesoutlier.m ├── get_pseudostacking_trends_withnewdata.m ├── get_pseudostacking_trends_withnewdata_andnewcriterion.m ├── get_pseudostacking_trends_withnewdata_andnewcriterion_noTGV.m ├── three_region_criterion_zoomed.png └── verify_new_pseudostacking_criterion.m ├── README.md ├── ReconstructionModel ├── isInTriangle.m ├── recon_fcn_v2_testing_script.m ├── reconstructionFunctionNPK.m ├── reconstructionFunctionNPK2.m ├── reconstruction_function_script0p35.m ├── reconstruction_function_script0p5.m ├── reconstruction_function_script0p5_STEPHENSETTINGS.m ├── reconstruction_function_script0p5_try_oldfun.m ├── reconstruction_function_script1p15_STEPHEN.m ├── reconstruction_function_testing_script.m ├── rotateOnAB.m └── rotateOnAB_v2.m ├── SIfigureScripts ├── DS10_SPcalibrated_tensorrot_strainmaps.m ├── DS26_SPcalibrated_tensorrot_strainmaps.m ├── DS2_SPcalibrated_tensorrot_strainmaps.m ├── fitting_schematic.m ├── fitting_schematic_DP.m ├── gaussianFBRprofile.m ├── make_DS12s2_heterostrain_map.m ├── make_DS3s2_heterostrain_map.m ├── make_cleaned_DS10s1_displacement_map.m ├── make_cleaned_DS10s1_triangulation_map.m ├── make_cleaned_DS10s2_displacement_map.m ├── make_cleaned_DS11s2_displacement_map.m ├── make_cleaned_DS12s2_displacement_map.m ├── make_cleaned_DS12s2_triangulation_map.m ├── make_cleaned_DS15s2_displacement_map.m ├── make_cleaned_DS18s1_displacement_map.m ├── make_cleaned_DS18s1_triangulation_map.m ├── make_cleaned_DS26s1_displacement_map.m ├── make_cleaned_DS26s1_triangulation_map.m ├── make_cleaned_DS2s1_displacement_map.m ├── make_cleaned_DS3s2_displacement_map.m ├── make_cleaned_DS3s2_triangulation_map.m ├── make_cleaned_DS4s1_displacement_map.m ├── make_cleaned_DS4s1_triangulation_map.m ├── make_cleaned_DS4s2_displacement_map.m ├── make_cleaned_DS4s2_triangulation_map.m ├── make_cleaned_DS6s1_displacement_map.m ├── make_cleaned_DS8s1_displacement_map.m ├── make_cleaned_DS8s2_displacement_map.m ├── make_cleaned_DS9s2_displacement_map.m ├── plot_displacement_partition.m └── revise_principal_angle_plot.m ├── SecondRevisionMisc ├── .DS_Store ├── Bias │ ├── 01192021NewBiasPlot_noredcircle.fig │ ├── 01192021NewBiasPlot_noredcircle.png │ ├── 01192021NewBiasPlot_withredcircle.fig │ ├── 01192021NewBiasPlot_withredcircle.png │ ├── bias_script_secondrevision.m │ ├── longbias_reader.m │ └── plotHalfDisplacementHexagon.m ├── LineProfiles │ ├── .DS_Store │ ├── 01192021_SPdisplacementProfile.png │ ├── 01192021_SPdisplacementProfile_0p26.fig │ ├── 01192021_SProtationProfile.png │ ├── 01192021_SProtationProfile_0p26.fig │ ├── 01192021_SPtracedata.mat │ ├── DS26_TGV_strainmaps_nodivideby2.m │ ├── HigherAngle │ │ ├── .DS_Store │ │ ├── 01202021_1p03angle_SProtationprofile.fig │ │ ├── 01202021_1p03angle_displacement_SPprofile.fig │ │ ├── DS2_TGV_strainmaps_nodivideby2.m │ │ ├── Parallel_tensile_displacement.fig │ │ ├── Perpendicular_shear_displacement.fig │ │ ├── rotationprofile.fig │ │ ├── xdispprofile.fig │ │ └── ydispprofile.fig │ ├── ImprofileSPdisplacementData.mat │ ├── RotationPlot.fig │ ├── SPtrace.m │ ├── SecondImprofileSPDataBetter.mat │ ├── WhereTheImprofileLinesWereDrawn.jpeg │ ├── improfile2SPxdisp.fig │ ├── improfile2SPydisp.fig │ ├── improfileSPxdisp.fig │ ├── improfileSPydisp.fig │ └── verify_annealing_DS26_noprefactor_newsettings_nodivideby2.m └── TriangulationGradients │ └── triangulation_uncertainty_secondrev.m ├── SensitivityBiasTesting ├── Bias2Simulation_9x9.fig ├── FirstBiasSimulationResults.fig └── bias_script.m ├── Simulations ├── DomainSizeSim │ ├── AA_1p1driver.m │ ├── LoggerProInverseFits.jpeg │ ├── SPsimdriver0p8.m │ ├── SPsimdriver0p9.m │ ├── SPsimdriver1p0.m │ ├── SPsimdriver1p1.m │ ├── SPsimdriver1p2.m │ ├── SPsimdriver1p4.m │ ├── SPsimdriver1p6.m │ ├── SPsimdriver1p8.m │ └── SPsimdriver2p0.m ├── makeSimulatedDisplacementDataset.m └── simulated_data_driver.m ├── StrainCalculationsAndAnnealing ├── .DS_Store ├── Analytic_strain_modeling2.mlx ├── Analytic_strain_modeling3.mlx ├── AnnealingScripts │ ├── verify_annealing_DS10.m │ ├── verify_annealing_DS15.m │ ├── verify_annealing_DS15_2.m │ ├── verify_annealing_DS18.m │ ├── verify_annealing_DS18_2.m │ ├── verify_annealing_DS2.m │ ├── verify_annealing_DS26.m │ ├── verify_annealing_DS26_2.m │ ├── verify_annealing_DS4.m │ ├── verify_annealing_DS4_2.m │ ├── verify_annealing_DS5.m │ ├── verify_annealing_DS7.m │ └── verify_annealing_DS8.m ├── ChiralFixedAnnealingScripts │ ├── .DS_Store │ ├── OriginalChiralFixed │ │ ├── verify_annealing_DS10_chiralfixed.m │ │ ├── verify_annealing_DS15_2_chiralfixed.m │ │ ├── verify_annealing_DS18_2_chiralfixed.m │ │ ├── verify_annealing_DS1_chiralfixed.m │ │ ├── verify_annealing_DS26_chiralfixed.m │ │ ├── verify_annealing_DS26_chiralfixed_noprefactor.m │ │ ├── verify_annealing_DS2_chiralfixed.m │ │ ├── verify_annealing_DS3_chiralfixed_tear.m │ │ ├── verify_annealing_DS4_chiralfixed.m │ │ ├── verify_annealing_DS5_chiralfixed.m │ │ ├── verify_annealing_DS6_chiralfixed_tear.m │ │ └── verify_annealing_DS8_chiralfixed.m │ └── newSettingsScripts_ChiralFixed │ │ ├── verify_annealing_DS10_newsettings.m │ │ ├── verify_annealing_DS15_2_newsettings.m │ │ ├── verify_annealing_DS18_2_newsettings.m │ │ ├── verify_annealing_DS26_newsettings.m │ │ ├── verify_annealing_DS26_noprefactor_newsettings.m │ │ ├── verify_annealing_DS2_newsettings.m │ │ ├── verify_annealing_DS3_newsettings.m │ │ ├── verify_annealing_DS4_newsettings.m │ │ ├── verify_annealing_DS5_newsettings.m │ │ ├── verify_annealing_DS6_newsettings.m │ │ └── verify_annealing_DS8_newsettings.m ├── Session2 │ ├── verify_annealing_DS10S2.m │ ├── verify_annealing_DS11S2.m │ ├── verify_annealing_DS12S2.m │ ├── verify_annealing_DS15S2.m │ ├── verify_annealing_DS1S2.m │ ├── verify_annealing_DS23S2.m │ ├── verify_annealing_DS24S2.m │ ├── verify_annealing_DS25S2.m │ ├── verify_annealing_DS26S2.m │ ├── verify_annealing_DS30S2.m │ ├── verify_annealing_DS3S2.m │ ├── verify_annealing_DS4S2.m │ ├── verify_annealing_DS8S2.m │ └── verify_annealing_DS9S2.m ├── StrainCalculationScripts │ ├── .DS_Store │ ├── DS1_cropped_strain.m │ ├── StrainCalcsPostColin │ │ ├── .DS_Store │ │ ├── 07262020_revised │ │ │ ├── .DS_Store │ │ │ ├── SPstrain_SP1_newdata.m │ │ │ ├── SPstrain_SP1_newestdata.m │ │ │ ├── SPstrain_SP1_orgdata.m │ │ │ ├── SPstrain_SP1_orgdata_minimalfilter.m │ │ │ ├── SPstrain_SP2_newdata.m │ │ │ ├── SPstrain_SP2_newestdata.m │ │ │ ├── SPstrain_SP2_orgdata.m │ │ │ ├── SPstrain_SP2_orgdata_minimalfilter.m │ │ │ ├── SPstrain_SP3_newdata.m │ │ │ ├── SPstrain_SP3_newestdata.m │ │ │ ├── SPstrain_SP3_orgdata.m │ │ │ ├── SPstrain_SP3_orgdata_minimalfilter.m │ │ │ ├── make_combined_SP_strain_plots.m │ │ │ ├── make_combined_SP_strain_plots_allnewdata.m │ │ │ ├── make_combined_SP_strain_plots_minimalfilter.m │ │ │ ├── make_combined_SP_strain_plots_newdata.m │ │ │ └── num23fixed │ │ │ │ ├── SPstrain_SP1_newestdata_23fixed.m │ │ │ │ ├── SPstrain_SP2_newestdata_23fixed.m │ │ │ │ ├── SPstrain_SP3_newestdata_23fixed.m │ │ │ │ └── make_combined_SP_strain_plots_23fixed.m │ │ ├── 07282020AB_AA │ │ │ ├── revised_AA_rotation.m │ │ │ ├── revised_AA_rotation_23fixedquant.m │ │ │ ├── revised_AA_rotation_minfilter.m │ │ │ ├── revised_AB_rotation.m │ │ │ ├── revised_AB_rotation_23fixed.m │ │ │ └── revised_AB_rotation_minfilter.m │ │ ├── get_SP_strain_postColin_soliton1_originaldata_hasmaxshear.m │ │ ├── get_filtermatched_AA_rotation_postColin.m │ │ ├── get_filtermatched_AB_rotation_postColin.m │ │ ├── get_filtermatched_SP_strain_postColin.m │ │ ├── get_filtermatched_SP_strain_postColin_allsolitons_alldata.m │ │ ├── get_filtermatched_SP_strain_postColin_allsolitons_originaldata.m │ │ ├── get_filtermatched_SP_strain_postColin_newdata_firsttrial.m │ │ ├── get_filtermatched_SP_strain_postColin_soliton2.m │ │ ├── make_regime_shaded_FBR_plot.m │ │ └── make_regime_shaded_FBR_plot_2.m │ ├── get_filtermatched_AA_rotation.m │ ├── get_filtermatched_AB_rotation.m │ ├── get_filtermatched_SP_strain.m │ ├── plotAAfixed_body_rotation.m │ └── plotAAshearstrain.m ├── TVmin_displacement.m ├── Uniaxial │ ├── DS3_uniaxial_strain_facet_plot.m │ ├── DS8S1_3Dhistogram.fig │ ├── extract_Stephen_strain_values.m │ ├── generate_strain_values.m │ ├── make_DS10S1_heterostrain_histogram.m │ ├── make_DS10S1_heterostrain_map.m │ ├── make_DS2S1_heterostrain_map.m │ ├── make_DS4S1_heterostrain_map.m │ ├── make_DS4S2_heterostrain_map.m │ ├── make_DS8S1_heterostrain_histogram.m │ ├── make_heterostrain_histograms_combined.m │ ├── uniaxial_strainfun_testing.m │ └── uniaxial_strainfun_testing2.m ├── Visualize_SP_strain.m ├── analytic_reconstruction_modeling.mlx ├── analytic_strain_modeling.m ├── analytic_strain_modeling.mlx ├── averagingDownsample.m ├── compute_strain_croppedDS7.m ├── estimate_sp_shear_DS7.m ├── generate_opposing_chirality.m ├── reproduce_Muller.m ├── simulated_data_driver_revisedVM.m └── test_filter_settings.m ├── TBLG_strain_vector_directions.m ├── TEAM1DS7DiffractionSI__integration_disks.mat ├── TEAM1Day1Dataset10__integration_disks.mat ├── TEAMI ├── .DS_Store ├── MultistartVideoDS4 │ └── make_multistart_video.m ├── permn.m ├── plotFullDisplacementHexagons.m ├── shiftFittingBounds.m ├── stabilize_displacement_field.m ├── team1_ds26_multistart_fit_locations.m ├── team1_ds4_multistart_fit_locations.m ├── team1_ds4_radialresidualsinterp_script.m ├── team1_ds7_radialresidualsinterp_script.m ├── team1_ds7_script.m ├── team1_hotspots.m ├── vector_equivalence_testing.m └── visualize_realspace_displacements.m ├── applyBeamstopCenterMasks.m ├── average_disk_shape_testing.m ├── beam_center_consistency.m ├── beamstop_zoomed_in_center.m ├── braggDiskRegistrationRecipe_innards.m ├── braggDiskRegistrationRecipie_1.m ├── braggDiskRegistrationRecipie_1_ARCHIVED.m ├── braggDiskRegistrationRecipie_2.m ├── bragg_disk_cross_correlation.m ├── calculateLatticeVectors.m ├── center_detection_via_hBN_driver.m ├── computeFullLatticeVectors.m ├── computeStrain.m ├── contourf_thresholded_slicemax.m ├── convMax.m ├── convertMaskedCoordsToOriginalCoords.m ├── convolution_overlap_study.m ├── cutROI.m ├── cutROI_fromPosition.m ├── cutROI_fromRanges.m ├── cutROI_from_shape_and_position.m ├── extendedTrigFittingFunctions__ARCHIVE.m ├── gammaPink.m ├── generateHexagonalLatticeMask.m ├── getAveragedDiskShape.m ├── getAveragedDiskShape_innards.m ├── getAveragedDiskShape_noIndices.m ├── getBeamspotCurve.m ├── getCOMofMASK.m ├── getCenterFromhBN.m ├── getFreehandMasks.m ├── getFullRadialPoissonMaxLikFit.m ├── getFullRadialPoissonMaxLikFit_bootstrap.m ├── getFullRadialPowerLawFit.m ├── getFullRadialPowerLawFit_logspace.m ├── getFullRadialPowerLawPred.m ├── getFullRadialPowerLawPred_bootstrap.m ├── getFullRadialPowerLawPred_logspace.m ├── getHexagon.m ├── getHexagonalLattice.m ├── getHexagonalWindow.m ├── getPixelSpaceAngle.m ├── getPowerLawFit.m ├── getROIKernel.m ├── getVertexAngle.m ├── get_radial_slice.m ├── guessInitialLatticeVectorsForIndexing.m ├── indexGraphenePeaks.m ├── ipin_fig1_notgreatregistration.fig ├── isInAngledSector.m ├── isInAngledThickRay.m ├── isInAnnulus.m ├── isInCircle.m ├── isInHexagon.m ├── jpin_fig2_notgreatregistration.fig ├── makeBeamstopCenterMasks.m ├── makeFilteredLinearDataFromImageMatrix.m ├── makeHexagonalLatticeMask.m ├── merge4thdim.m ├── mtit.m ├── mycolormap.m ├── orderHexagonVertices.m ├── orientHexagonToMatch.m ├── plotAllRods.m ├── plotDPWithRegistration.m ├── plotDPandDisks.m ├── plotStrain.m ├── python_peakfinding.m ├── radial_powerlaw_fit_beamcenter_determination.m ├── recipie_1_driver.m ├── registerDatacube.m ├── registerInterferenceRods.m ├── relIntensityThreshold.m ├── removeTooNear.m ├── rotateHexagon.m ├── shiftImage.m ├── simulate_beamspot_movement.m ├── simulate_strain.m ├── sortGraphenePeaks.m ├── testCutROI.m ├── testHexagonalLatticeMask.m ├── testIsInCircle.m ├── testIsInHexagon.m ├── testLoadDMFile.m ├── testLoadh5file.m ├── test_hexagonal_lattice_mask.m ├── testingStirling.m ├── thickenMask.m ├── 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