WIRSCHAFFENWISSEN–HEUTEFÜRMORGEN

MuhRec and KIPTool under the hood

AndersKaestner::PaulScherrerInsAtut

SINE2020WP101stCoordinaAonmeeAng,VilligenPSI,CH,April2016

Neutron imaging

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Additional modes: -  Real-time imaging

-  Stroboscopic imaging

-  Tomography

-  Energy selective imaging

-  Grating interferometry

Basic Principle: -  Spatial domain acquisition of transmitted neutrons à Images

-  The universal attenuation law applies

Neutron imaging

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Neutron imaging experiments

Data

•  Pre-processing

•  Noise suppression (first level)

•  Artifact reduction

•  Scattering correction

•  Experiment related processing

•  Interpretation/estimation

•  Tomographic reconstruction

•  Image processing

•  Noise suppression (second level)

•  Segmentation

Visualization Modeling

Data processing tasks for imaging

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Imageprepara-on Imageanalysis

Referencing

Enhancement

TransformsAcquisi-onàObserva-on

DenoisingAr-factremoval

Registra-onPhysicalcorrec-ons

Segmenta-on

Classifica-onFeaturecharacteriza-on

Materialcharacteriza-on

Displacementquan-fica-on

Timelapseanalysis

Massquan-fica-on

Etc.

Instrumentdependent Applica-ondependent

Fusion

Which tools are used today?

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CT reconstruction •  Octopus

•  GridRec (+IDL GUI )

•  MuhRec

•  Astra, TomoPy, TomoJ etc

3D processing, analysis, and visualization •  VG Studio, Aviso

•  ParaView, Drishti, MeVisLab, KNIME, VisTrails

•  KipTool (image processing for special applications)

•  Matlab

Projection processing •  ImageJ/FIJI

•  QNI scattering correction (Hassanein, 2006)

•  nGI Tool

•  Matlab, IDL

•  Python

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MuhRec and KIPTool

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MuhRec:CTreconstructor

KIPTool:Generaltoolfor3Dprocessing

ImagingTool: A collection of small tools

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TomoMerge Datarenamer

GenericconversionVolumeSlicer

nGI Tool

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Efficientprocessingofphasesteppingimagesfromagra-nginterferometerWillonlybeaddedtothesuiteoncethealgorithmsarepublished

• Allapplica-onsareavailablefor- Windows(64bit),Ubuntu14.04,MacOS

• GUIisimplementedusingQt5.x•  Implementa-onlanguageC++(startedusingC++11)• Mul--threading- MainlysolvedusingOpenMP(notwithClangonMac)- FirsttestsusingC++11threads

• DevelopmentinQtCreatoronallpla^orms(usingQMake)• Nocommerciallibrariesareused• Un-lnowonlyfewunittestsimplemented…• Limiteddocumenta-on

General implementation information

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Configura-on

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The module system

FactoryProcessingchain

Module A

Module B

Module C

Module DLib 1Module AModule D

Lib 2Module B

Lib 3Module C

Data

Result

Configuration script

GUI Configuration

•  Dynamicloadrequestedmodules•  Parameterizemodules

Configura-onstructsarefilledusing•  GUIwidgets•  XML-scripts

Processingengine

•  Loaddata•  Executechain•  Storeresult

Coremodulesystem-  Moduledescrip-on(xml)

-  Dynamicloadingofmodules-  OSspecificdetailssupported

-  Abstractinterface

-  Supports-  Singlemoduleloading-  Chainloadingusingfactory

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The module system classes (non-GUI)

ConfigBaseList:ModuleConfig

ModuleConfig

LibnameModulenameModuleparameters

Configura-on(General)

FactoryEngineBuildsList:ModuleItem

Feeds

Processing environment (Application specific)

ModuleItemRef:ProcessModuleBase ProcessModuleBase

KiplModuleItem ReconModuleItem

KiplProcessModule

ReconProcessModule

A B C D

A B C D

Modules(General)

Modules(Applica-onspecific)Processingalgorithms

Theseaddnewprocessingandanalysisfunc8onality

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Module configurator widget

Modulelist Parameterlist

Featuresmodulelist•  Add/deletemodules•  Enable/disablemodules•  Rearrangeorder•  Suppor-ngconfigura-ondialogs

Featuresparameterlist•  Parametersappearfortheselectedmodule•  Add/deleteparameters•  Editparametername•  Editvalues(currentlyonlyasstrings)

Configura-ondialogexamples

BasedonQWidget

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Flow chart Module dialogs

Selectmoduleinconfigwidget

CheckifGUIlibisavailable

Throwexcep-on

TrytogetModuleDialogfromlib

Throwexcep-on

ModulesareinlibModules.xyzDialogsinlibModulesGUI.xyz

Opendialogwithcurrentparameters

•  ModuledialogsarebasedonQDialog•  Dialogscanoperate

•  Withoutimages,fasteropening•  Withimages,thepreviousstepsintheprocessingchainwillbeexecuted

MuhRec

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•  GUIbasedCTreconstruc-ontool•  Basedonfilteredbackprojec-onwithparallelbeamgeometry•  Freelyconfigurablepreprocessingchain- Normaliza-on- Ar-factreduc-on(SpotsandRings)- Datacorrec-on- Projec-onfilter- Inspectors

•  Newfunc-onalitycaneasilybeaddedasmodulesforpre-procandrecon•  Supportedfileformats:fitsand-ff•  Mul-OSsupport(Windows,Linux,MacOS)•  CanberunusingscriptsorCLI

MuhRec Specifics

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Some common preprocessing modules

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• Normaliza-on

• Spotcleaning

• Ringcleaning

• Reconstruc-onfilter-Ramp+apodiza-onfilters

Raw

Raw Cleaned

Cleaned Difference

Today:•  Thebackprojectorismul-threaded•  Most-meisspentonar-factremoval- Thereisroomforimprovement

Muhrec: Some word about performance

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Execu-on-meonasinglethread(2011)

• Addconebeamgeometry•  Improvepreprocessing-me- ar-factreduc-onis-meconsuming

• Additera-vereconstruc-onmethods- PredefinedSIRT,DART,SARTforsingledat- Addsupportforaprioriinforma-on

• Addsupportfor4DCT(dataflow+regulariza-on)•  ImproveGUIstability(inkl.improveuserfriendliness)•  Improveuserdocumenta-on• AddHDFsupport(e.g.NeXus,Matlab,others?)• Supportfor6Ddata?• Porttoclusterbasedrecon• Pythonscrip-ng(forrapidprototypingmodules)

MuhRec next steps

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KIPToolwasdevelopedtoprovideauserinterfacetoimageprocessingalgorithms•  Worksmainlywith3Ddata•  Loadastackofimages•  2Dsliceinspec-on•  Basedonachainprocessor•  Resultscanbecomparedwithoriginal- Histogram- Profiles- Difference

•  Severalmodulelibraries

KIPTool specifics

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Base•  Scaledata•  Dataclamping•  Dosecorrec-on•  Volumeprojec-on

Classifica-on•  Doublethreshold•  FuzzyC-Means•  Removebackground

Advancedfilters•  ROFfilter(ISS)•  Non-lineardiffusion•  Non-localmeans

PCA•  PCAfilter(experimental)

Porespace•  Poresizedistribu-on(experimental)

TheROFfiltermodelisanedgepreservingdenoisingfilter

KIPTool using ROF (ISS filter)

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Plots and information

Demonstration ROF filter

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10 iterations 50 iterations 500 iterations

•  Addmoremodules- Instrumentrelatedprocessing- Registra-on- Segmenta-on- Analysis- Quan-fica-on

•  Changeprocessingchaintonetwork- Nodeeditor- Mul-pleimagesupport

•  2Dand4Dsupport•  Scrip-nginPython- Usingmodules- Callinglibraryfunc-ons

KIPTool next steps

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•  Displayoffloa-ngpointdata•  HandlesrectangularROIs•  IntensitymeasurementsinROI•  Semngdisplayedintensityintervalusingdialogorrightmouse•  Showsintensityandmouseposi-onastool-p•  Canlinksemngswithotherimageviewers•  Supportsplotsandmarkers•  BasedonQwidget•  CanbeusedinPDFreports

Image viewer widget

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• Abasicplomngwidget• Mul-pleplotsandcolors• Horizontalandver-calmarkerslines• Zoomfunc-on• Glyphsondatapoints• BasedonQwidget• CanbeusedinPDFreports

Plot widget

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Current libraries – an overview

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Visualiza-oniss-llanopenques-onCurrentlycommercial(veryexpensive)fullfeaturedtoolsareused•  VGStudio•  Aviso

Theysolvemanytasksbutfailwithmorespecifictasks-  4Ddata(-meseriesofvolumes)-  6D(vectorsin3D)-  Mul-variatevisualiza-on

ThesetopicswillbetargetedduringaplannedworkshoporganizedwithCOSTac-onMP1207:VisualanalysisofdynamicprocessesPlace:RigiKulm,CH,January2017

3D and 4D Visualization

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Wir schaffen Wissen – heute für morgen

WiththecurrenttoolswehaveaniniAalsuiteoftoolsforneutronimaging……Thedevelopmenttowardsmorecomplexexperimentcondi-ons.…Flexibilitytoaddnewfeatures.…Alreadyausercommunity.