User manual for MuhRec
Contents
1. 2 5 The geometry list It is possible to store the current configuration in the geometry list using the application menu item Geometry This can be used to test the effect of different settings without losing the original settings Each parameter set will be stored with the central slice to make comparison easier If you have reconstructed several slices on different places you can use the entries of the list to calculate the axis tilt MUHREC3 USER MANUAL DRAFT o 0 Stored configurations Compute tilt 19 10 55 2015 05 14 Center 304 Center 301 04 Tilt 0 382 Slice 100 Pivot 100 R2 1 Compute ROI 19 12 04 2015 05 14 No ROI Center 304 04 Slice 100 19 12 38 2015 05 14 Center 302 04 Slice 400 Clear selected Select all Cancel OK Figure 2 5 The Geometry list dialog 10 3 Detailed descriptions 3 1 Processing modules The processing module play a central roll in the reconstruction They are used to manipulated the projection data prior to the back projection task In the following sections each module is described The order of the modules can be arbitrarily configured In some cases it makes sense to maintain a certain order among the modules This reordering can be done in the GUI by dragging the modules in the pre processing module list Unfortunately there is a bug in the GUI package that may cause the application to crash The reordering can also be made in the config file since2. projpath Volumes DataDisk P20140142 destpath projpath 04_evaluation 20141126 20 MUHREC3 USER MANUAL DRAFT muhrec Users kaestner Applications muhrec3 app Contents Mac0S muhrec3 cfgpath projpath 04 evaluation 20141126 recon roots xml from subprocess import call from math import fmod firstproj 1 firstframe 0 lastframe 3 for i in range firstframe lastframe select projection sub set firstindex projections firstindex str firstproj i 180 lastindex projections lastindex str firstproj i 1 180 set file mask for the slices matrixname matrix matrixname frame_ 04d i slice_ tif adjust the reconstruction angles to alternating between 0 180 and 180 360 angle fmod i 2 180 scanarc projections scanarc str angle str angle 180 call the reconstruction call muhrec f cfgpath firstindex lastindex matrixname scanarc This script assumes that you have a well configured Recon xml file and that the data is acquired as a long sequence e g a time series of CTs 21 4 Continued development MuhRec is continuously developing to adapt to new challenges at the neutron imaging beamlines at Paul Scherrer Institut Unfortunately it is not only new development but also bug fixing To fix bug the input from users is important so I kindly ask you to report problems when the software misbehaves For the continued development it also important with feedback regarding improveme
3. F ba Configure the Full Log Y Use dose correction Y Use look up table computing Cancel DK Figure 3 1 Configuration dialog for the log norm module Object file libStdPreprocModules so 11 MUHREC3 USER MANUAL DRAFT 3 1 2 SpotClean2 Spots are the most frequent outlier artifacts encountered in neutron imaging These appear as line artifacts in the reconstructed data There is a large benefit in using the spot cleaning algorithm since this increases the signal to noise ratio in the matrix significantly Line artifact cleaning is parameterized by two parameters the threshold level and a fuzziness parameter around the threshold Mostly the fuzzy width parameter is set to about 10 of the threshold Original Cleaned Figure 3 2 The effect of spot cleaning The spot cleaning is parameterized by two parameters the threshold and the mixing fuzziness The threshold defines the intensity of the pixels to correct All pixels with values exceeding the threshold will be corrected The second parameter is used for interpolation between the estimated correction values and the original image Pcorrected 1 w Poriginal W Destimate the weight function is a sigmoid centered about the threshold level This means that some pixels below the threshold will also be involved in the correction The spot cleaning configuration wizard helps you to find the correct levels of the two pa rameters A threshold func
4. feature Finally you can also set the pixel size of the projections This information is needed if you want the gray levels of the pixels to have the unit cm The pixel size is also written as resolution in the slice images The amount of memory required for the reconstruction is estimated to give you an idea if the task is feasible for your computer You can control the memory usage by changing the geometry of the reconstructed image i e change the margins or number of slices The region of interest is marked in the projection preview image The region used for dose computation is also marked in this display 2 2 2 Saving the parameters Once you have set all parameters it is recommended to save the parameters You save the parameters by selecting save or save as in the file menu Alternatively you can also press CTRL S which performs the same action In a way the parameter file is a documentation of your reconstruction It also allows you to load the parameters at later moment if you would like to do adjustments or reconstruct a new part of the samples You can also use the parameter file for command line reconstructions and batch processing For more details about the command line mode please read section 3 6 The saved parameters can either be loaded into the GUI by using the File Open menu or without GUI in the command line option When you start a reconstruction the used parameters are automatically save in the file Cur rentRe
5. on the reconstruction time 21 C Intended new features 1 Flip and 90 rotations 2 True rotation of the projections 3 Center estimation by reconstruction 4 Add a module for QNI for the projections QNI is a method to reduce the impact of scattering on the data It often makes it possible to quantify the water content in a sample 9 Your suggestions 28 D Known bugs and limitations D 1 Limitations 1 The back projection core only works on a single thread 2 Center of rotation can not be found for translated projection data D 2 Bugs e The reconstructor may crash when the number of slices is not a factor of 4 e The translated center reconstruction does not reconstruct correctly near the center of rotation This is especially noticeable when tilt correction is activated e First and last slice in a block appears to have different intensity Not verified The module selection list in add module is not cleared when a new object file is opened 29
6. reconstructs parallel beam geometry tomographies The software includes the following features e Two modes of operation GUI and command line e The GUI helps the user to set up the reconstruction and execute the processing e Artifact cleaning algorithms to remove ring and line artifacts A guide to find center of rotation and tightest margins Acquisition axis tilt correction e Handles image formats common at neutron imaging beamlines e Various options for normalization MuhRec3 is the next step of my reconstruction tool development It provides more flexibility in terms of configuration The design of the reconstruction engine has an open API that makes it possible for users to add their own processing modules In addition the user can configure order in which the preprocessing modules are executed Due to major changes in the architecture of the software it was not possible to maintain backwards compatibility with the configuration files from the first version of MuhRec 1 3 Node locked software MuhRec is free of charge and I intend to keep it so But since I want to have control over the distribution I decided to include a node locking routine The node locking gives me better contact to the user community The license key you get can only be used on the computer that generated the unlock code 1 4 Some words about the name The name MuhRec is derived from the sound of the cow in German Muh and Reconstructor Th
7. 3 1 3 MedianMixRingClean Ring artifacts are with line artifacts the most common artifact in a CT slice This is a basic method for correcting ring artifacts It identifies outliers in the average sinogram and corrects them by the local median threshold Sets a threshold on the local variance that identifies an outlier that would cause a ring Default value 0 01 width Sets a smooth weighting interval for the replacement Typically this value is about 10 of the threshold Default value 0 001 Object file libStdPreprocModules so 3 1 4 ProjectionFilterSingle This is a central module for the filtered back projection algorithm It applies a ramp filter combined with a apodization window line wise on the projection data cutoff The cut off frequency can be used to improve the signal to noise ratio of the reconstruc tion As it has a low pass effect it will smooth the edges in the image It can take values between 0 and 0 5 Default value 0 5 filtertype This parameter controls the shape of the apodization filter There are several window shapes implemented ramlak shepplogan hanning hamming and butterworth Default value hamming order This parameter is only relevant for the Butterworth filter where it defines the exponent of the filter and thus controls the filter shape Default value 0 13 MUHREC3 USER MANUAL DRAFT Configure median mix ring clean Original Processed Difference Sinogram profile Lambda M
8. 3 11 Possible acquisition axis tilts 3 6 Reconstructing from the command line In addition to the GUI you can also start MuhRec from the command line This can done by typing muhrec3 f parameters xml The file parameters xml contains all settings needed for the reconstruction This is also the same type of files written by GUI In appendix B an example of the parameter file is given The command line option is useful for batch reconstructions The parameter files for all reconstruction jobs can be prepared with the GUI In some cases there are only a few parameters that change between the data sets In this case you can add these parameters on the command line using the format muhrec3 f parameters xml blockl parameterl valuel block2 parameter2 value2 The block is the xml block in the parameter file userinformation system projections matrix and parameter is the parameter you want to modify with value Please note that each pa rameter argument must be a single string each space will be interpreted as delimiter for a new argument Therefore if you want to change an array parameter you have to use to enclose the argument Eg muhrec3 f parameters xml projections roi 10 10 100 100 Muhrec use less memory when it is operated in CLI mode Invoking Muhrec from a script Sometimes it is convenient to use a script to run muhrec Here is an example using python usr bin env python print Processing some frames
9. EM a Sigma 0 00500 Refresh Cancel OK Figure 3 4 The median mix ring clean configuration dialog usebias The ramp filter cancels the DC term of the spectrum The effect is a bias in the reconstruction By activating this parameter a small value is added to the DC component Default value true Configure the Projectigg Filter oe Select filter type Hamming Cut off Frequency 0 5000 Filter order 0 Y Use DC bias Cancel OK Figure 3 5 The projection filter configuration dialog Object file libStdPreprocModules so 3 1 5 ISSfilter This is an experimental module used to smooth the projection data The module uses an inverse scale space filter to filter the individual projections It seems to improve the SNR with maintained edge sharpness The filter has some problems with the numerical stability at least it is difficult to tune There will be a tuning wizard in the future N Number of solution iterations Default value 10 alpha 0 25 lambda 1 tau 0 02 Object file libStdPreprocModules so 14 MUHREC3 USER MANUAL DRAFT Configure the 155 filter Original Processed Difference Error plot Histogram 4 4 lambda 0 01000 ll alpha 0 00100 r Iterations 50 bi tau 0 00100 E Y Scale data Auto scale Slope 0 00012 Intercept 16516 50000 Refresh Cancel OK Figure 3 6 The projection filter configuration dialog 3 1 6 AdaptiveFilter Samples with high a
10. HREC3 USER MANUAL DRAFT The contrast and brightness can be adjusted by dragging using the right mouse button If you pause while the right mouse button is pressed a tool tip shows the current brightness and contrast A level dialog appear if you press 1 when the viewer is active You can also mark regions in the viewer and press the Get ROI button related to the viewer 3 3 The projection data MuhRec supports input projection data in the formats TIFF FITS and Matlab binary Nor mally the filenames of the projections are sequentially ordered and each file has a base name and an index number To enter the file name in the projection entry field you should use the format base_ ext The number of tells MuhRec how many zeros to use in the formatting The s can be placed anywhere in the name string The extension indicates which file format to use Below the file name field the file interval can be entered with first and last file index These indices will both both included In addition there is also an entry to set the increment This increment can be used to decrease the number of projection in test reconstructions This saves time but do not forget to repeat the reconstruction with all projections before you start the final reconstruction An alternative way to enter the projection data with a text file The advantage of this approach is that you can use any filename and for each projection and you can specify the acqui
11. User manual for MuhRec A Kaestner June 14 2015 Contents 1 Introduction la Frodu O Ns e egg eds Ge aut Ene ave Gh tase Gk ae da hse as Bie ek Boks Woe A Kos Fod ES ques Gets ewes hes nih WEF eo Gt OS we BE A ot ae Bee eo ee Be 1 3 Node locked software 2 2 1 4 Some words about the name 2 A First Reconstruction Zl Brojeci NORMA LION us rij dt Sve Bee BW OS Bee Sek an ee A a ko A 2 2 Set projection information and geometriy 2 2 1 Setting the geometry aa sed se a do GAO 6 A di Be EA we es Bs 2 2 2 Saving Lhe parameters a y po Eat E e a a RE we a eee z 2 3 Configure the processing chain Dios Preprocessing CHAIN ssa bos ee ee a ee eS E Doses LO back Projector i que 4 8 e Se bt doe eb ee Ea DAS RCCOMSGRUCHION s a apso bus o sia Hy ie om Be ee Ae Ok ONA Os ae Wee a EE 2 4 1 Start the processing s corsario AA DAD Timali e Lhe data i poses o er Ai wt ee ES e de the ie dd ea DOS Doe Ehe geome oi asa cars ir es mag Trat as E a a en 3 Detailed descriptions dolo FProcessine modules s s s peiie ai e Se be A k leds Fallot Nor e sore ad ai ein e E NL SEDA RE a Be Ee deli DPOC e gp esd apanr a eaa eaae 09 Y L 3 1 3 MedianMixRingClean aoaaa gle TR So Ge R O ee doe Tn e E O SA Projecuonkilteroindie ps upa gs Ega E das E DEE A dni Del MO MILE jy sienna ah dee tay eB dg io ee ee Bee RE SO Adaptive bite sussa Se ee E Be ee el
12. applies a polynomial to each pixel value This is used to correct for beam hardening effects in the reconstructed image Object file libStdPreprocModules so Coefficents The coefficients of the terms of the polynomial starting with ag i e there must be PolynomialDegree 1 values Default value 0 0 1 0 PolynomialDegree Sets the polynomial degree the module can handle up to the 8th degree Default value 1 3 1 11 SpotRingClean Ring cleaning by spot cleaning is an experimental module that is not finished It cleans some of the rings but the performance is still not satisfying Object file libStdPreprocModules so gamma Threshold level in the detection image Default value 0 01 iterations Number of times the filter should be repeated Default value 1 sigma Width of the mixing interval Default value 0 001 3 1 12 TranslatedProjectionWeighting This module weights the projections near the center of rotation to provide a smooth stitching of the projection data when you reconstruct data that is acquired with the center near the edge This is a method to increase the FOV at maintained resolution Object file libStdPreprocModules so weightfunction sigmoid width 5 16 MUHREC3 USER MANUAL DRAFT Configure correction polynomial x Original Processed Difference Polynomial plots Polynomial order 4 a 0 00000000 al 1 00000000 a2 0 10000000 aj 0 10000000 a4 0 00100000 Refresh N Fig
13. ation angle 32 00 Start reconstruction Figure 2 3 The process chain configuration tab 2 4 Reconstruction 2 4 1 Start the processing Once the parameters for the reconstruction have been set you can start the reconstruction by pressing the Start Reconstruction button There are however two modes to consider for small data sets you can do the reconstruction in interactive mode This means that you after the finished reconstruction can adjust the gray levels and select destination folder file name and file format When the selected matrix is to large for the available memory a dialog that gives you the options to reconstruct directly to disk with the setting on the matrix tab or to cancel the started reconstruction If you select the direct streaming option for the reconstruction there will be no output in the slice display Often it is recommended to make a small test reconstruction to check the quality of the selected parameters Select between 16 and 64 slices in a relevant region of the sample and reconstruct them It may take some iterations until you have everything as you want it When you are satisfied with the result you can reconstruct the whole data set in a single run This may take some time 2 4 2 Finalize the data When the reconstructor finished processing the data you are automatically directed to the Matrix tab figure 2 4 In this mode you see a histogram of the reconstructed data The vertical li
14. con xml which is save in your home directory This file will automatically be loaded when you start Muhrec next time 2 3 Configure the processing chain 2 3 1 Pre processing chain When the geometry is configured you can switch to the processing tab figure 2 3 On this tab you can configure the chain of preprocessing modules This means you can add new modules if your data requires some special treatment and you can edit the module parameters IN the current version this can only be done in entry fields In the future it is planed to add wizards to guide the configuration of the more complex modules 2 3 2 The back projector It is also possible to change back projector and configure its parameters The most important parameter is the buffer size This parameter has a direct effect on the memory consumption during the reconstruction On a 32 bit system it may be needed to change the buffer to a smaller value when wide projections are reconstructed MUHREC3 USER MANUAL DRAFT MuhRec2 CT reconstructor Ss E Datei Bearbeiten Configuration Hilfe Project information Projections and geometry Processing Matrix Messages Preprocessing modules Active Module name Parameter Value SY FullLogNorm gamma 0 01 MedianMixRingClean noma Ma ES maxlevel 12 MM ProjectionFilterSingle o minlevel 0 1 sigma 0 001 Slices Budd Delete Properties Add Delete Back projector Back projector module MultiProjBP Preferences ab Rot
15. dcfirstindex gt 1 lt dcfirstindex gt lt dccount gt 5 lt dccount gt lt roi gt 600 400 1700 432 lt roi gt lt doseroi gt 300 600 350 800 lt doseroi gt lt scanarc gt 0 360 lt scanarc gt lt projections gt 20 MUHREC3 USER MANUAL DRAFT lt matrix gt lt dims gt 1100 1100 32 lt dims gt lt rotation gt 0 lt rotation gt lt serialize gt false lt serialize gt lt path gt home kaestner work svn lt path gt lt matrixname gt tablet_ tif lt matrixname gt lt filetype gt TIFF16bits lt filetype gt lt firstindex gt 0 lt firstindex gt lt grayinterval gt 1 0 728486 lt grayinterval gt lt matrix gt lt processchain gt lt preprocessing gt lt module gt lt modulename gt FullLogNorm lt modulename gt lt sharedobject gt libStdPreprocModules so lt sharedobject gt lt active gt true lt active gt lt parameters gt lt uselut gt false lt uselut gt lt usenormregion gt true lt usenormregion gt lt parameters gt lt module gt lt module gt lt modulename gt SpotClean2 lt modulename gt lt sharedobject gt libStdPreprocModules so lt sharedobject gt lt active gt true lt active gt lt parameters gt lt gamma gt 0 03 lt gamma gt lt iterations gt 1 lt iterations gt lt maxlevel gt 12 lt maxlevel gt lt minlevel gt 0 0 lt minlevel gt lt sigma gt 0 005 lt sigma gt lt parameters gt lt module gt lt module gt lt modulename gt MedianMixRingClean lt modulename gt lt
16. e ES we id Sl Basic him Cleo a dana A abe Be So A RS eke AE dello Mabtascaler ue o a ADIA as A Sw eee q RA A A o e DLI General Een ss Da srs Soe E ES A eee RS eee de eee a SL dO Pol normal Correc a ura praia EE BNE Oe ERC AI E E EE Ee SiS DO Rune CIC sua ES det EA A E Be LE 3 1 12 TranslatedProjectionWeighting 3 1 13 WaveletRingGlean 2 246 scsi 8 4 ae oh aa ew ee k Sia ONA NE 4 oo 8 ob ot ds e Es a E os E ee EE we ae ee a ollo AP LOJCCHOMINGDECLON 2 ear Md 6 2 ae oS we eS E 3 1 16 Dave E LOJCCUIONG S pisa Ya Bb we oi eR SR aS ee a Dice A a sd Ed amp Bock oe dep eR Se ASE Eb AA 3 94 Theprojection data e use a e ab Oe ee Boh OR ALA OE ee oe cs Ted 3 4 Spatio temporal tomography a a a a dd SEWGCOLPEChION ga bites A do amp Be wet Ai ce a Bek ado al toe Tenda OE 3 6 Reconstructing from the commandline 4 Continued development ree KB DS O oo CONN NNN ooo 11 11 12 13 13 14 15 15 16 16 16 16 16 17 iii 17 18 18 19 19 19 20 22 U O U gt MUHREC3 USER MANUAL DRAFT License Parameter file format Intended new features Known bugs and limitations Dal GAOS er GA at LE oe hk a ee oe ee OO ee ae ee A ED DOS oa a eat dE EM we eee A ee A we ee ee 24 25 28 1 Introduction 1 1 Introduction The development of MuhRec started when 1 2 Features MuhRec is a reconstructor for computed tomography It
17. eneral format is basename ext where the base name can be any string the extension is used to MUHREC3 USER MANUAL DRAFT MuhRec2 CT reconstructor ma He ufa E Doom No tip No rotation e Reference images Reference path Etomo Same as projection path e m ca O usamos of an x Empr Geometry s 65 E nea re TE ce am a oo um m com om o so pos Center Position 568 00 lt O PTA noo e o Resolution mm pixe 0 0135 Memory usage 381Mb matrix 148 buffers 234 system max 6000Mb Preview Start reconstruction Figure 2 2 The projection and geometry tab determine image file type and must be correctly specified Finally the are place holders for the file index The number of place holders defines how the zero padding should be used Some examples proj_ tif will give the filenames proj_00 tif to proj_99 tif and thereafter proj_100 tif etc If you omit the at all the indices will be inserted after the base name and before the extension without zero padding Once you have defined file names and path you have to set the first and last projections as well as the file stride The stride is used to reduce the number of projections for test purposes when you want a quick reconstruction The first index can be any positive number smaller than the last projection index Below the projectio
18. ere are two reasons for the Muh Firstly the author lives in the Swiss village Muhen which by the way has nothing to do with cows The software was to large extent developed on the train commuting between Muhen and Paul Scherrer Institut The development distance can hence be determined to be about 20000 km The second reason is that the cow is the national proudness of Switzerland and the cow says Muh The third reason is that there are many cows surrounding PSI 2 A First Reconstruction 2 1 Project information When you start MuhRec you will see the project information tab figure 2 1 This tab allows Datei Bearbeiten Configuration Hilfe Information Project P11001 Sample Unknown item Instrument ICON Operator Anders Kaestner Description No comment Figure 2 1 The project information tab you to enter information about the experiment The name you enter in the fields will be written to the image file headers of the reconstructed slices 2 2 Set projection information and geometry The next step is enter information about the projection files and the image geometry This is done in the Projections and geometry tab figure The projection data is the input to the reconstruction You can also provide reference images here To enter the information you have to enter the path of the directory which contains the projection data Then you have to enter the file mask of the projection files the g
19. n information you find some fields for rotation flip and skip projections Theses fields are currently only place holders for up coming features which are not even imple mented The reference files are entered in the same manner as the projections Both open beam and dark current images are required to located in the same directory You also have to set the first reference image index and the number of references These numbers are set for both open beam and dark current image separately If you don t have any reference images just set the number of references to 0 When all file parameters are set you can click the preview button to see the projection in the display area to the right MUHREC3 USER MANUAL DRAFT 2 2 1 Setting the geometry The geometry is essential for the reconstruction The most important is the center of rotation which has to be determined to sub pixel accuracy Other parameters defines the number of slices and the margins of the projections The projection configuration dialog helps you to find the minimal margins and the center of rotation If your projection data was acquired with a tilted axis of rotation it will have an impact on the reconstructed data Since this means that the center of rotation depends on the slice position i e only the slice you tuned center of rotation for will be correctly reconstructed Small tilts lt 1 can be corrected The correction for larger tilt angles is still a pending
20. nes in the histogram shows the interval used to display the reconstructed slice in the viewer These levels will also be used to in the conversion to integer formats You can change the gray level interval in the entry fields on the top MUHREC3 USER MANUAL DRAFT F MuhRec2 CT reconstructor Datei Bearbeiten Configuration Hilfe Project information Projections and geometry Processing Matrix Messages Matrix settings Gray levels Low 0 0493 B High 0 2437 ki Y Auto levels Y ero xo 380 ki yo 150 e xi 999 g y1 799 ki Slice index 11608 Histogram Entropy 4 47657 Output Destination path recon Slice mask objects AHHH tF Filetype TIFF 16 bits Start reconstruction Figure 2 4 The matrix display tab A slider can be used to browse through the slices By sliding through the slices you can inspect the slices to check that the gray interval is correctly set You can also see if there are any artifacts in your data Once you are satisfied the image settings and reconstruction quality you can save the slices To do this you have to select the destination folder and enter the file mask for the slices The mask has the same format as the projection data i e base ext The extension must be entered manually as it is not adapted to the selected file type The last selection to make is the file format which can be either tiff with different bit depths or matlab binary
21. nts of existing and new features So if you have any comments that you would like to share I appreciate if you send them to me I cannot promise that I will implement everything but I will at least consider it 22 Bibliography 23 A License Definitions The software refers to any revision of MuhRec The author Anders Kaestner is referred to as the author Any person who installed and intends to use or uses the software is referred to as the user e The software source code binaries and any supporting material is the property of the author e The user is allowed to install and use the software free of charge e It is not allowed to decompile and or modify the files in the software distribution e The software is delivered as is The author gratefully receives bug reports and feature requests but can not promise any updates In case of updates the user will be notified e The author takes no responsibility for the use of the software and the accuracy of the results e The user is strongly discouraged from using the software for medical applications e If you use the results in a publication The following publication should cited Anders P Kaestner MuhRec A new tomography reconstructor Nuclear Instruments and Methods in Physics Research Section A Accelerators Spectrometers Detectors and Associated Equip ment Volume 651 Issue 1 21 September 2011 Pages 156 160 doi 10 1016 j nima 2011 01 129 24 B Paramete
22. ply Figure 3 9 Dialog to tune the ring correction using wavelet ringclean Left panel is original mid shows the processed sinogram and the panel to the right shows the difference 3 1 16 SaveProjections This module save the projection data in the current state of processing as a set of 32 bit tif images Object file liblnspector Modules so path Path to the destination folder filemask File mask of the written files It shall always contain a block of amp s as placeholder for the file index Default value projections_ tif imagetype Selects the file type of the projection data H can be either projections or sinograms Default value projections filetype Selects the precision of the data in the written files It can be 8 or 16 bit unsigned or 32 bit floating point Default value 32bit floating point o 0 Dialog Destination path Users kaestner test projs Browse File mask proj _ tif File type 32 bit Float TIFF Image type Projections Figure 3 10 Dialog to set the values of the SaveProjections module 3 2 The Viewer The viewer area on the right hand side of the application main window is used to display projections and reconstructed slices If move mouse pointer to the viewer and wait shortly a tool tip message will appear It tells you the position and intensity on position you point with the mouse This is useful to determine threshold levels guiding algorithms like the margin detector 18 MU
23. r file format The parameter file is formatted with xml and is divided into subsections Here the default parameter file is shown lt reconstructor gt lt userinformation gt lt operator gt Anders Kaestner lt operator gt lt instrument gt ICON lt instrument gt lt projectnumber gt P11048 lt projectnumber gt lt sample gt Curse tablet lt sample gt lt comment gt No comment lt comment gt lt userinformation gt lt system gt lt memory gt 6000 lt memory gt lt loglevel gt message lt loglevel gt lt system gt lt projections gt lt dims gt 2048 2048 lt dims gt lt resolution gt 0 0135 0 0135 lt resolution gt lt firstindex gt 1 lt firstindex gt lt lastindex gt 625 lt lastindex gt lt projectionstep gt 1 lt projectionstep gt lt repeatline gt false lt repeatline gt lt scantype gt sequential lt scantype gt lt imagetype gt projections lt imagetype gt lt center gt 568 lt center gt lt translation gt false lt translation gt lt tiltangle gt 0 lt tiltangle gt lt tiltpivot gt 0 lt tiltpivot gt lt correcttilt gt false lt correcttilt gt lt filemask gt tablet_ fits lt filemask gt lt path gt home data P11048_tablet tomo lt path gt lt referencepath gt home data P11048_tablet tomo lt referencepath gt lt obfilemask gt ob_ fits lt obfilemask gt lt obfirstindex gt 1 lt obfirstindex gt lt obcount gt 5 lt obcount gt lt dcfilemask gt dc_ fits lt dcfilemask gt lt
24. sharedobject gt libStdPreprocModules so lt sharedobject gt lt active gt true lt active gt lt parameters gt lt threshold gt 0 01 lt threshold gt lt width gt 0 001 lt width gt lt parameters gt lt module gt lt module gt lt modulename gt ProjectionFilterSingle lt modulename gt lt sharedobject gt libStdPreprocModules so lt sharedobject gt lt active gt true lt active gt lt parameters gt lt cutoff gt 0 5 lt cutoff gt lt filtertype gt hamming lt filtertype gt lt order gt 0 lt order gt 26 MUHREC3 USER MANUAL DRAFT lt usebias gt true lt usebias gt lt parameters gt lt module gt lt preprocessing gt lt backprojector gt lt module gt lt modulename gt MultiProjBP lt modulename gt lt sharedobject gt libStdBackProjectors so lt sharedobject gt lt active gt true lt active gt lt parameters gt lt ProjectionBufferSize gt 16 lt ProjectionBufferSize gt lt SliceBlock gt 64 lt SliceBlock gt lt SubVolume gt 1 lt SubVolume gt lt parameters gt lt module gt lt backprojector gt lt processchain gt lt reconstructor gt Most of the parameters can be set with GUI There are however some exceptions e lt memory gt amount of memory available for reconstruction unit mb e lt projectionbuffersize gt number of projections to process simultaneously e lt sliceblock gt max number of slices to process in one processing block The buffer parameters have direct impact
25. sition angle for each projection The format of the file is angle0 lt tab gt fileA ext anglel lt tab gt fileB ext angleN lt tab gt fileXYZ ext The you use a text file to specify the projection data You can use the file index numbers to select intervals in the file list The first line in the file has index 1 Stepping does not work Once you have entered all projection information you can press the Preview button and the first projection will appear in the viewer The displayed projection is the raw projection 3 4 Spatio temporal tomography For samples which change over time it is not possible to 3 5 Tilt correction When the turn table and detector are not aligned there will be an error in the reconstructed data For small deviations this error can be corrected by adjusting the center of rotation for each slice In MuhRec you have two parameters for the tilt correction The first is the axis tilt angle and the other set the pivot point relative to the image The pivot is used for long samples where the turn table is located far away from the detector For a single data set this parameter is less important than when you have several scans that you want to merge after the completed reconstruction It is not possible to correct for both detector and pivot tilt simultaneously in the current version Figure 3 11 shows the two different detector rotations 19 MUHREC3 USER MANUAL DRAFT Adetector Apivot Figure
26. spect ratio between width and thickness have an orientation dependent signal to noise ratio This filter adaptively applies more smoothing to regions with low transmission Figure 3 7 The effect of the module for adaptive filtering The unfiltered image a reconstruc tion with the adaptive filter activated b and c is difference image between the images a and b lambda Threshold at with the smoothing takes place The value of lambda makes sense in the interval 0 0 1 0 Default value 0 1 sigma Defines the width of the mixing interval This value should mostly be less than 0 1 Default value 0 05 size Width of the smoothing filter kernel Default value 5 Object file libStdPreprocModules so 3 1 7 BasicRingClean The basic ring clean subtracts a high pass filtered average sinogram from all sinogram This a rather crude way of ring correction but it will cancel some of the rings Object file libStdPreprocModules so 15 MUHREC3 USER MANUAL DRAFT 3 1 8 DataScaler The data scaler makes a linear scaling of the data k x m This can be useful if have preprocessed images that are save in a 16 bit data format Object file libStdPreprocModules so offset The offset m of the straight line Default value 0 0 slope The slope k of the straight line Default value 1 0 3 1 9 GeneralFilter Object file libStdPreprocModules so size 3 type box 3 1 10 PolynomialCorrection This module
27. the modules are executed in the order they are entered The modules can be configured by clicking on a module in the module list Then a list of parameters for the module is shown Click on the parameter value you want to change and enter the new value Don t forget to press enter to confirm the new entry A module can also be temporarily disabled by unchecking the active check box Then it remains in the configuration but does not contribute to the processing chain This option is useful if you want to speed up the processing a little It can also be used to demonstrate effect before and after adding the module 3 1 1 FullLogNorm In most cases a complete projection data set also contains open beam and dark current images The location and names of the images are entered separately under the Projections tab Here you can also set the number of available reference images The full normalization operation is computed using p log F He 3 1 D los tpc This equation includes correction for variations in the neutron dose This module computes the flat field correction of the projections The correction is followed by the negative logarithm The module uses the reference images entered in the projection information tab uselut Selects if the computation should be supported by a LUT to gain some speed Values true false usenormregion Selects if the norm region should be used for dose correction Values true false
28. tion plot in the cumulative histogram shows in which interval the correction will work When you execute the correction the detection map and the the corrected image will be shown The amount of corrected pixels will also be displayed This wizard will only show you the region of interest you marked in the projection geometry setting Therefore you may want to increase the number of slices a while for a better overview during the tuning process of the spot cleaning gamma This is a threshold value setting an allowed variance maximum that discriminates local image variations from actual outliers Typical value 0 03 iterations This is currently an unused parameter that would iterate the cleaning procedure N times Typical value 1 maxlevel Data clamping parameter values greater than this level are set to the defined level Default value 12 minlevel Data clamping parameter values less than this level are set to the defined level Typical value 0 sigma A width parameter to allow smooth mixing of the values around the threshold Default value 0 005 Object file libStdPreprocModules so 12 MUHREC3 USER MANUAL DRAFT Configure spot clean Original Processed Difference Histogram of detection signal Gamma 0 0400 Sigma 0 0010 Iterations 1 Maxspotarea 100 ak Min value 0 1000 Max value 12 0000 ab Refresh Cancel OK Figure 3 3 The spot clean 2 configuration dialog
29. ure 3 8 The projection filter configuration dialog Cancel DK 3 1 13 WaveletRingClean This ring cleaning module works in the sinogram domain It does the cleaning using a combi nation of wavelet and fourier transforms The current version introduces new artifacts as a consequence of bad edge processing in the wavelet transform I e this module is still under de velopment The filter bank could also gain of the addition of more and longer filter descriptions Object file libStdPreprocModules so decnum Number of decomposition levels Default value 5 sigma Width of the Gaussian that forms the stop band Default value 0 1 wname The name of the wavelet base Default value daub25 3 1 14 CountNANs This module is mainly for debugging use It counts the number of pixels set to NaN This can be helpful to identify which module causes the numeric errors in your processing chain Object file liblnspector Modules so 3 1 15 Projectionlnspector This module is not fully implemented but is intended to open a display window that shows the projections in their current condition Object file liblnspector Modules so 17 MUHREC3 USER MANUAL DRAFT o 0 Configure wavelet ring clean A MI il 2 Wavelet name daub15 verticalfft lt SS rm ti AA gt gt _ o A e e Lambda 2 gt Sigma 0 05000 Ap
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