The visrock user manual
Contents
1. 4 8 1 2D Median filtering Median filtering is a well known technique for suppressing extreme pixel values in 2D images Every pixel value is replaced by the median of all pixel values inside a square box surrounding the respective pixel The width of this box can be selected via the field labeled Median x y and must have a value of 2 or higher The default value of 0 indicates that no median filtering will be applied Median filtering is rather efficient at eliminating spurious features single outliers or small groups of outlier pixels It has the additional advantage of having rather limited collateral effects as compared to other averaging and smoothing techniques It will however slightly degrade the lateral resolution in the image especially at larger box widths 2D median filtering is a reversible technique inside visrock in the sense that it is applied on the fly only to the intermediate data just being plotted to screen or saved to file i e to the image analysis results and not to the original image data residing in memory Therefore reverting to a width value of 0 will reproduce exactly the original noisy data This convenience comes at a price in terms of efficiency The median filtering operation is carried out anew every time that the image is being plotted This takes a little time on 24 Correlations between images T T T T T T TP T Image nr Image nr Figure 9 Map of co2. 23 This function may therefore be useful to detect e g a sudden partial beam loss during exposure of a flat field image series 4 7 2 Correlation functions A correlation coefficient between a pair of images is a single scalar number whereas a correlation function for a pair of digital images is again a 2D distribution with the same number of pixels in x and y as the original images The central element has the same value between 0 and 1 as the trivial correlation coefficient while the value of all other pixels indicate how much similarity could be achieved by shifting one of the two images by the corresponding number of pixels with respect to the other Clicking on the button labeled Correlation functions allows to calculate a cor relation function between the currently selected image and a second one to be selected from a list of filenames presented in a new window see Fig 11 After confirmation and calculation which may take some time the resulting 2D correlation function is saved as a postscript file which will be displayed on screen using ghostview on Linux UNIX only As the correlation function has complex values there will be several plots presenting the real and imaginary components as well as the absolute values as 2D distributions and several 1D projections of the same data see Fig 12 4 8 Noise reduction Fig 13 shows the various options available for suppressing noise in 2D images inside visrock
3. A few additions like high pass and low pass filters will be inserted in the near future Further suggestions from users are always welcome 31 5 Using visrock III Special functions for specific ap plications visrock contains a few functions which are individually optimized for very specific appli cations and may well be ignored by general users 5 1 Functions for Rocking Curve Imaging 5 1 1 Dark field correction In rocking curve imaging as in tomography and presumably most other fields of X ray imaging it is important to subtract an image of dark counts caused by camera dark current readout noise intentional offset etc from each one of the actual experimental images This task can be automated by using the field labeled Dark field in the upper left of the visrock GUI The name of an image file containing a dark field image can either be entered directly into this field via the keyboard or selected interactively from a list of files on hard disk via the button on the right The dark field filename must be entered before reading the actual non dark image files The dark field data will be read into memory and displayed on screen for immediate check Upon completion of the reading process of the main list of images the dark field data will then be automatically subtracted from each and every image in the series before further processing This may take some time depending on the computer system being used Ins
4. for one value of w at a time 3 1 1 Reading individual images Single images can be read from hard disk by clicking on the Read CCD files button in the upper right of the visrock GUI Multiple images can be selected by using the SHIFT and or CTRL keys and will be read in sequence after clicking OK 3 1 2 Reading large series of images When reading large series of images it may be more convenient to specify the images to be read via a txt file containing the names of all the image files in a single column This can be done by clicking on the Read File list button 3 1 3 Supported image formats The format of the image files will be automatically analyzed by visrock from the file name extension The following image formats are understood by visrock tiff Standard digital image format jpg Standard digital image format gif Standard digital image format png Standard digital image format edf Esrf Data Format produced by 2D detectors such as the Frelon cameras ASCII header plus uncompressed binary image data mccd Image format produced by MarReserach CCD cameras in widespread use in protein crystallography Regular tiff format plus extra binary header b16 Slightly exotic digital image format apparently produced by CCD cameras from PCO gqe Binary image format produced by the Spectra program developed by Thorsten Kracht and used at many HASYLAB beamlines 9 xdr Even more exotic gen
5. 2048 pixels 2 Bytes typical case for ESRF Frelon cameras this means that no more than 200 230 images can be analyzed at once leaving some RAM for IDL itself and other system applications Larger sequences can either be analyzed piecewise e g in four quadrants or on systems with even more memory such as the ESRF indigo machines with 16 GB of RAM Screen visrock can be run on screens having at least 1024x768 pixels but is optimized for larger screens 1600x1200 is ideal 2 4 Installation visrock does not need to be installed in any way Just copy the downloaded file visrock sav to the directory of your choice that s it 2 5 Launching visrock 2 5 1 With an IDL license Start IDL by typing idl on the Unix prompt or by clicking on the appropriate icon under Windows On the IDL command line type restore lt path gt visrock sav where lt path gt is the path to the directory where you saved visrock sav Provided that you have correctly set the IDL_PATH environment variable you should now see the visrock GUI see Fig 1 2 5 2 Without an IDL license Starting from IDL version 6 0 on precompiled IDL programs such as visrock sav may be run in the IDL Virtual Machine VM even without an IDL license For further expla nations see the file idlvm pdf provided in the help subdirectory of your IDL distribution To start visrock in the IDL VM proceed as follows Under Linux On your
6. available orig data Plot the intensity data contained at the respective pixel position in the original images as a function of image number angular position ROJI integral Plot the sum of intensity values in all pixels visible in the map plotting area When the map is in the completely unzoomed state the sum of intensities in the entire image s is plotted ROI min Plot the minimum intensity value reached in any pixel across the current zoom area as a function of image number angular position ROI max Plot the maximum intensity value reached in any pixel across the current zoom area as a function of image number angular position spatial stddev Plot the standard deviation of intensity values in a local surrounding of the pixel selected by clicking as a function of image number Useful e g for investi gating whether the noisyness of a camera image changes with time or temperature When this option is selected an additional stddev radius input field will appear below the plot allowing to select the width of the local surrounding with a standard value of 1 pixel to the right and left sum_x log data for ROI Expert feature undocumented so far sum_y log data for ROI Expert feature undocumented so far 4 2 Curve plotting options The appearance of the Intensity versus angle curves displayed in the right drawing area can be changed via the buttons below the plot 16 Figure 3 Curve plotting op
7. before final confirmation Save these data Store the plot data to an ASCII data file A default filename of tmp dat will be suggested but can be changed before final confirmation The file will contain two columns of data and one row for each data point in the plot Real data Plot the original histogram data default Fourier data Plot the 1D Fourier transform of the original data rarely useful for histogram data xlog Logarithmic x axis axis of pixel values ylog Logarithmic y axis axis of frequency of occurrence 22 Clearup Replot Show histogran Correlation coefficients Spatial R values Correlation functions Figure 8 Some map analysis functions FWHM Automatically analyze the width of the highest peak in the plot and write the result to a corner of the plot min and max Specify a restricted range for the y axis in absolute frequency of occurrence numbers 4 6 Line profile extraction from images One dimensional value profiles can be extracted interactively from the 2D map plots via mouse clicks A double click with the left mouse button will extract a horizontal line profile z values as a function of x coordinate from the map crossing the clicked pixel A double click with the right mouse button will extract a vertical line profile z values as a function of y coordinate 4 7 Correlations Correlation coefficients measure the degree of similarity between two im
8. command line type idl vm lt path gt visrock sav where lt path gt is the directory where you stored visrock sav Visrock C 2001 2002 Daniel Luebbert HASYLAB DESY pe aj E A ee ee caf C 2291 edf etc 7 files 0 0 204 203 Intensity a u No N o 2 N N o o 1986 z 21 20 19 18 17 I6 Image number Plot of oria data Figure 1 Appearance of the visrock GUI in Linux style The two plot areas are for image display left and curve display right The meaning of the remaining buttons and fields will be explained in subsections 3 and 4 Under Windows Drag and drop the visrock sav program onto the IDL VM icon on your desktop In both cases you will have to click away the IDL VM splash screen Please be aware that a few limitations exist in the unlicensed mode of IDL as described in idlvm pdf In particular IDL s execute function will not work which means that commands entered via the execute text field at the bottom of the visrock window cannot be carried out 3 Using visrock I Basic functionality for beginners Basic usage of visrock usually includes three steps Data input image analysis and output of results most often as postscript plots 3 1 Data input reading images The visrock program works on a 3D data set intensity data as function of e g x y and w These are usually read into memory as a sequence of 2D images intensity data as a function of x and y
9. e demagnification by a factor of 2 is performed by clicking once with the middle mouse button The clicked pixel will become the center More exactly Clicking and releasing on the same pixel without intervening motion 20 of the new image which will be twice as wide and high as before provided that enough data are available A double click with the middle mouse button will perform a complete unzoom i e all of the available data will be displayed on screen Figure 6 Arrow buttons for shifting the region of interest In order to shift the region of interest to an adjacent area without changing the scale magnification factor use the arrow buttons Fig 6 The outer 8 buttons allow to shift the region horizontally vertically or diagonally The central button labeled o will zoom in by a factor of 2 4 4 4 Mirroring Image inversion The map display can be mirrored in either the x or the y direction by activating the Invert x and or Invert y buttons see Fig 5 4 4 5 Image rotation The map display can be rotated by an arbitrary angle by entering a value in the field labeled Rotate by deg see Fig 5 Note that in the case of rotation by odd angles parts of the display area may be void for lack of data will parts of the available data disappear beyond the border of the plotting area 4 4 6 2D Fourier transforms Instead of the original data their 2D Fourier transfo
10. 0 4 4 l l 1 l l 1 n l l i 200 100 0 100 200 200 100 0 100 200 Correlation function of home luebbert Data 1999 06_99 caf C 0006 edf gz vs home luebbert IWwaf fEAT E MOMBedlifebhert Data 1999 06_99 caf C 0006 edf gz vs home luebbert Data 1999 06_99 caf C 0008 edf gz orrelation map projected onto x shift axis T T T a S TT S S TT Sum of correlation values real part over y 1 1 200 100 0 100 200 x Correlation function of home luebbert Data 1999 06_99 caf C 0006 edf gz vs home luebbert Data 1999 06_99 caf C 0008 edf gz Figure 12 Result of calculation of correlation function between a pair of images Full correlation function real part full correlation function absolute value and projection onto the horizontal axis 4 8 4 3D variance filter Unlike Dezingering the 3D variance filter function for noise reduction will combine the values of several spatially adjacent pixels For each pixel the average and the standard deviation of pixel values in a local environment cube of 3 pixels side length is calculated and compared to the central pixel If the pixel value deviates from the average by more than and interactively entered tolerance value times the standard deviation then it is replaced by the mean This algorithm is realized in two alternatives The parallel version treats all pixels identically and always takes the original pixel values when calculating the local envir
11. 2002 Available online at http ww mpimf heidelberg mpg de kabsch xds D LUBBERT T BAUMBACH J HARTWIG E BOLLER and E PERNOT pum resolved high resolution X ray diffraction imaging for semiconductor quality control Nucl Instr Meth B 160 4 p 521 527 2000 A R LANG and A P W MAKEPEACE Reticulography a simple and sensitive technique for mapping misorientations in single crystals J Synchrotron Rad 3 6 p 313 315 1996 J LOVELACE E H SNELL M POKROSS A S ARVAI C NIELSEN N H XUONG H D BELLAMY and G E O BORGSTAHL BEAM ish a graph ical user interface for the physical characterization of macromolecular crystals J Appl Cryst 33 4 p 1187 1188 2000 P MikuL K D LUBBERT D KORYT R P PERNOT and T BAUM BACH Synchrotron area diffractometry as a tool for spatial high resolution three dimensional lattice misorientation mapping J Phys D Appl Phys 36 10 p A74 A78 2003 E Pacot Diffraction Enhanced Imaging applied to Breast Tissue PhD thesis Universit Joseph Fourier Grenoble 2003 W PRATT Digital Image Processing Wiley New York 2nd edition 1991 Z SILAGADZE A new algorithm for photopeak searches Nucl Instr Meth A 376 p 451 454 1996 42
12. The visrock user manual Daniel Lubbert July 23 2006 Id visrockManual tex v 1 1 2005 08 02 14 54 41 luebbert Exp Contents 1 Introduction what the visrock program can be used for 1 1 Structure of this manual a Ves cent ee OS ee Oe ee ee Preconditions to using visrock 20 Obtainine visrock s Se Sete bong Sea Me ig Sha He ie ARA OES ee 2 21 ACCUSES POUCH o te p aa n e A Re ot ead wt ard es herd e atl 2 3 Systemi requirements e a dio a doe die a ese de Beas ee ete a eG L 24 Installation 3 2 402 4 3 9 A 2S 4 2 RR A A oe ee eee 2 9 UCI VeRO sc o A sheds E A clasts Se ae Tas Gk Ae ok th ete ia Using visrock I Basic functionality for beginners 3 1 Data input reading images lt b fogs ade lke e Poa ee I ater ae 3 2 mage analysis options leas re are lada ere ea ee els a 3 3 Saving the results to disk 305 e a SE ous Ge i ee 3 4 Terminating the program 2 2 A Bale ee ee ll Using visrock II Advanced functionality for experienced users 4 1 Curve analysis options 1 a Bad a Abe Ba ee Ae ed 4 2 Curve plotting options artes Hace he De gh A ee od DA ek A 4 3 Image Plotting options 224 awd 3 s ai A A O AA AXIS AIMEEGS roate yee erT Se Sea ke Eas es Me GPa aed Os GEL ang Sab ea a He Ash Histogram display oie th nie amp ised aw ae oe Beare ae Coe ee Be aai 4 6 Line profile extraction from images e Age Correlations e a e Bay a O Ges A a rr q 478 NOISE reduction 4 24 4 of am
13. a functions menu In the extra window that appears see Fig 4 select appropriate values for the variables X_UNIT_NAME and X_SCALE_FACTOR the length of one pixel in the unit defined by X_UNIT_NAME and similarly for y The same window also allows to select the character size to be used in the two displays and in the legends and to switch on 1 or off 0 the display of various titles and subtitles Finally the nature and format of the map legend display can be influenced via this window 4 4 1 Color scale Plot range selection The color scale in the maps can be adjusted so as to maximize contrast and highlight specific features Three mechanisms are available One can either enter lower and upper limit values manually in the fields labeled Minimum value and Maximum value As a consequence any pixel values beyond these limits will be represented with the same 18 A E je TES X Figure 4 The Edit Plot Options window allowing to define axis units among others color as the limits themselves In this way the entire range of available colors contrast is concentrated on this interval of values As an alternative the values can be defined interactively by using the two vertical sliders to the left of the map plotting area The third most automatic way is to define min and max values in terms of per centiles After entering the required numbers in the fields labeled Minimum percentile an
14. able X ray intensity exposure time temperature etc This is a software manual not a camera characterization handbook We will therefore restrict the discussion to a few hints on how visrock can help in the analysis of such data assuming that the appropriate measurements have already been performed The noise level in a series of theoretically identical images e g a set of primary beam images recorded under identical conditions can be evaluated by using the standard deviation image analysis option see also p 13 Probably even more useful is the option noise lt gt Poissonian which compares the experimental variance in the data to the one expected when assuming Poissonian noise The resulting map will show where the variance is real i e caused by the incident beam statistics and where it is artificial i e caused by deficient noisy camera pixels Camera sensitivity linearity and dark current can all be quantified from a series of 36 primary beam images recorded with increasing exposure time or decreasing attenuation factor The analysis of such data is then performed with the Linear fit image analysis options The following result maps are of interest Linear fit Slope This shows how the camera pixels react to increasing incident X ray dose i e the sensitivity and its uniformity across the field of view Linear fit Background This option extrapolates the camera signal to zero incident int
15. ages They can have values between 0 no similarity and 1 complete correspondence Correlation functions are a more general concept telling whether two images can be made to be similar after a lateral 2D shift 4 7 1 Correlation coefficients and R values The button labeled Correlation coefficients will trigger the calculation of correla tion coefficients between any pairs of images in the series of N images currently loaded into memory The result is a real and symmetric N x N matrix of correlation coefficients which will be displayed as a 2D map in a separate window see Fig 9 This function is useful e g when inspecting a series of flat field images in tomography which should all be representing the identical distribution Considerable breaks in the 2D field of correlation coefficients may indicate an uncontrolled change in experimental conditions during exposure of the flat field series A similar concept well known to crystallographers are the so called R values be tween pairs of images They are calculated by pixel wise summation of relative differences between pixel values in the two images One of the images is defined as a reference while the other is the sample Therefore the resulting N x N matrix is asymmetric Apart from this the result is mostly equivalent to the case of correlation coefficients with the difference that R values are additionally sensitive to changes in overall intensity values
16. can perform a few tasks for preparing experimental data for reconstruction and for checking data integrity Fine Slicing or Super fine Y slicing Measuring the mosaicity of mostly protein crystals along all directions of reciprocal space by simultaneously recording rocking curves from a great number of crystallographic reflections using a CCD camera covering a wide range of exit angles BSLOO Diffraction enhanced imaging DEI Recording projection radiographs of a possibly non crystalline sample with a crystal analyzer as an additional optical element in the exit beam at a series of angular positions along the rocking curve of the analyzer crystal see e g Pag03 Reticulography Visualizing lattice irregularities in a crystal by monitoring the distortion of a rectangular grid pattern in X ray diffraction topographs recorded at several different sample camera distances LM96 Detector calibration visrock includes features for testing and quantifying the charac teristics of CCD cameras and other digital area detectors in terms of reproducibility and noise level linearity sensitivity and spatial homogeneity of response These can be determined from various series of dark field and flat field images The visrock program is a graphical user interface GUI it is entirely based on a point and click strategy The main aim is to simplify tasks that occur frequently and repetitively in image sequence analysis No keyboard i
17. ch image separately and is carried out first 4 8 3 Dezingering The field labeled Dezinger when filled with a value gt 0 will activate the Dezingering function This is a noise reduction technique that tries to eliminate spurious high pixel values zingers based on a standard deviation criterion The value entered roughly rep resents a multiple of standard deviations that can be tolerated as statistical deviations more highly deviating values will be eliminated For this to work a set of N at least 2 independent images theoretically represent ing the identical true image but distinct due to noise are required This function is particularly useful for treating dark field or primary beam images The algorithm is based on BTG99 assumes spatial homogeneity of noisyness and works iteratively until convergence is achieved and a best compromise image is found The calculation works independently for each pixel in the images adjacent pixels are not related to each other 27 Correlation function real part lin scale Correlation function absolute value lin scale T T T T 7 I T T I T 300 J H E 200 El m 0 1332 g m 1 053E 07 m 0 1023 m 0 01764 m 0 07131 m 0 03529 m 0 0403 m 0 05293 100 4 m 0 009372 El m 0 07057 m 0 02160 m 0 08822 m 0 05256 m 0 1059 m 0 08353 m 0 1235 0 1145 0 1411 0 1455 E 0 1588 0 1764 0 1764 100 El 4 200 El 3 30
18. d Maximum percentile see Fig 5 the program will automatically translate these into limits in terms of absolute pixel values Percentile values must lie between 0 and 100 As an example min and max percentiles of 5 and 90 mean that the lowest 5 and the highest 10 of pixel values will be flattened mapped to the corresponding limiting color This is particularly useful when a small number of outlier pixels zingers would otherwise spoil the automatic selection of color scales 19 Minimum value 0 0000 Minimum percentile 9 0000 F Map log Invertx w Do corr resol Rotate by deg 10 000 Eti Invert y Don t corr resol Maximum value 0 0000 Maximum percentile 3 000 Figure 5 Map plotting options selection 4 4 2 Linear logarithmic scaling Aspect ratio When the button Map log is pressed the color scale of the map shown in the left plotting area is chosen on a logarithmic scale This allows to obtain more image contrast in regions of weak intensity Choosing log scaling will cause problems when parts or all of the map are in the negative value range as may happen for position of maximum maps for example When the button is not active the color scale is chosen linearly this will enhance the visibility of the strongest peaks The button just below it labeled 1 1 will activate the maintain aspect ratio func tion This means that images with different numbers of pixels along the x an
19. d y axes will be plotted in a rectangular area with dimensions on the screen roughly proportional to the respective number of pixels When this button is not active images will be plotted in a quadratic regions on screen often making better use of the available display space 4 4 3 Zooming and unzooming By default all of the available image information is represented in the display Details can be magnified by choosing an area of interest AOI An AOI is defined interactively by clicking with the mouse Place the mouse pointer over one of the corners of a rectangular AOI press the middle mouse button or in case your mouse has only two buttons the left and right buttons simultaneously move the mouse pointer to the diagonally opposed corner of the AOI to be defined while keeping the button s pressed and release During the move the present size of the AOI just being defined will be visible as a bright rectangle overlaid on the image After releasing the new magnified plot will automatically be displayed on screen The center of the zoomed area can be shifted in the horizontal vertical or any diagonal direction by using the transfer buttons see block of 3 x 3 buttons in the lower right of Fig 3 This will leave the magnification zoom factor unchanged An exception is the central button labeled o which will not shift but increase magnification by a factor 2 in both directions The inverse operation unzooming i
20. data can be used for embellishing other plots by pressing the Mask wafer area button and then selecting the corresponding analysis option 5 1 3 Correction of maxpos maps for dispersion effects The position of maximum maps in Rocking Curve Imaging only partly reflect the sample curvature since they also contain instrumental effects In order to correct for this the Do corr resol button can be used Note that this button is available only when the maxpos analysis option is active After activating the correction option the program will ask for input data describing the experimental circumstances monochromator sample reflections geometry After confirmation visrock will calculate a correction map display it as a postscript file and subtract it from the raw maxpos map The correction can be undone by pressing the Don t corr resol button The calculation is based on the following formulae To be completed TODO Explain angular correction TODO Bild einbinden Figure 14 Input window for parameters describing the experimental geometry 5 2 Functions for Tomography visrock does not perform 3D reconstruction from projections This can be done by pro grams like HST However visrock can be used for preparing experimental projection images for reconstruction by HST This is particularly useful when working at beamlines which are not yet optimized for tomography where unexpected misbehaviour of optics
21. e reading process can be specified in a separate window see Fig 2 From top to bottom the most important choices are all parameters must be integer numbers bin_factor Rebin original images i e reduce their number of pixels via averaging by this factor The x and y dimension will be treated alike i e reduced by the same factor Must be an integer use every Nth file only Read only image files nr 0 N 2N and disregard files nr 1 N 1 etc Helps to save RAM and considerably speeds up the reading process by at least a factor N Must be an integer wait time Ifthe next file to be read is not found on hard disk e g because it is just being read out from the camera wait x seconds and try again before giving up Helpful when starting a reading process while the series of images is still being recorded x start x stop y start y stop Keep only a restricted area of the original images in memory and discard the outer regions Helpful in order to save memory space when the features of interest occupy only parts of the image surface Values must be 0 N 1 10 XEditList K Cancel TODA See S ae E a a A S ESA Figure 2 Popup window allowing to specify details of the image reading process The remaining fields of the window shown in Fig 2 will be discussed in Chapter 5 3 2 Image analysis options In the left drawing area 2D maps can be plotted which represent sections or
22. ensity i e it shows an alternative form of dark field to be compared to the one recorded with closed shutter Linear fit Chi This option shows whether or not the data set for each individual pixel could be fitted by a linear slope If yes low values of CHI the respective pixel shows a linear reaction to increasing incident dose which is most likely to be the desired behaviour 37 6 Planned future developments of visrock Here is an incomplete list of things that could and maybe will be implemented in visrock in the future e RC and extraction even for maps in inverted mode e More automatic normalization to monitor counts from edf file headers e Save memory space by cropping Display first file of series let user zoom to ROI allocate space only for ROI e 2D lattice tilt analysis la MLKO03 e Detector calibration Check correction for spatial distortion of tapered CCD cam eras e Advanced 3D rendering of the entire data stack e Multi peak analysis beyond the mere number of peaks per pixel e Segmentation of 3D data identifying coherent crystallites even if overlapping in space 38 7 List of known bugs 7 1 Bugs IDL crashes after you selected a large gt 200 number of individual files via the Read CCD files button This appears to be an IDL bug which occurs quasi predictably for file numbers above 250 300 at least on Linux systems No solution has been found so far A wo
23. eral file format somehow device independent read and writ ten by older IDL programs in use at BW4Q0HASYLAB In addition to the above and as a default if the file name matches the standard for none of the above visrock can analyze a general binary image format consisting of a H Byte header which will be ignored plus a rectangular array of NxM pixels with L Bytes per pixel The integer numbers H N M and L will be requested interactively until the expected number of Bytes N M L H matches the actual file size As an extra feature visrock can read compressed zipped copies of all available image formats This will work primarily on Linux systems it may or may not work under Windows It is particularly useful with edf images which are uncompressed in their native form unlike jpg or png and therefore waste enormous amounts of hard disk space Currently gz and bz2 compressed formats are supported When visrock encoun ters a compressed image it is first uncompressed to a temporary file and then read as usual Decompression is usually rather fast some tenths of a second even if the original compression took considerably longer Note that for this to work two conditions must be fulfilled e The appropriate decompression program must be found in the PATH gunzip or bunzip2 e You must have write permission on the tmp directory 3 1 4 Input details After selection of the files to be read a few more details of th
24. g part of visrock is in many ways similar to the Beamish program LSP00 although it is based on xds rather than on mosf1m 34 The main idea of the method is to collect rocking curves for many crystallographic reflections simultaneously This is done by recording diffraction patterns with the standard rotation method and a CCD camera but using a very small step width Each of the many Bragg spots needs to be located and indexed This is done by an initial indexing step using the xds program Kab02 The remaining task carried out by visrock is to extract the rocking curve for each reflection from the individual images apply the Lorentz correction and an additional geometry correction output the reflection profiles plus a big data array containing HKL FWHMs and many more After some initial enthousiasm the Fine Slicing project was abandoned because it was found that the method did not provide more information than a set of classical rocking curves but wasted more beam time given an appropriate multi circle diffractometer hard disk space and processing resources The documentation will therefore not be completed although the corresponding functions in visrock do work 5 4 Functions for Small angle scattering and general Crystallog raphy For scattering patterns recorded either by the rotation method in crystallographic data collection for structure determination or by small angle x ray scattering SAXS it is often interesting to
25. messages to be output here but some others don t If you observe an error message please copy and paste it into an email to the author also describing as much as possible of the circumstances If you get an error but no message then be patient and try again If and when you are convinced that it is a reproducible bug please send a short email to the author so it can added to the list of known bugs 40 8 Impressum Author Daniel L bbert Daniel Luebbert gmx de Send your comments and remarks questions if any suggestions for improvement and donations directly to the author Send your complaints to dev nul1 3If you are not a Linux guru please note This is a joke Al 9 Literature references References BSLOO0 BTG99 Her80 J h02 Kab02 LBHO00 LM96 LSP00 MLK03 Pag03 Pra91 Sil96 H D BELLAMY E H SNELL J LOVELACE M POKROSS and G E O BORGSTAHL The high mosaicity illusion revealing the true physical character istics of macromolecular crystals Acta Cryst D 56 8 p 986 995 2000 S L BARNA M W TATE S M GRUNER and E F EIKENBERRY Calibra tion procedures for charge coupled device x ray detectors Rev Sci Instr 70 7 p 2927 2934 1999 G HERMAN Image reconstruction from projections Academic Press New York 1980 B JAHNE Digital Image Processing Springer Heidelberg 5th edition 2002 W KABSCH XDS Program package
26. nput of any kind is required a simple mouse will suffice as an input device Among the functions that can be executed in this way are sorted roughly from simple to more complex e Reading image data from a large variety of file formats e Color plotting of scalar i e intrinsically black and white images to screen or to postscript output files Interactively adjustable color scales either linear or logarithmic Plot range selection based on absolute numbers or on percentile values Playing movies of image sequences Format conversion of grayscale images e g from edf to png from tif to edf and many more for single images or entire image series Interactive zooming specifying areas of interest with the mouse Monitoring the evolution of the intensity value in individual pixels along an image sequence file series or of the average intensity of a group of pixels Interactive extraction of local or regional Rocking Curves Automatic peak detection in extracted profiles Determination of peak half widths FWHM in profiles Gaussian fitting of profile peaks Line profile extraction from images in horizontal or vertical direction Horizontal and vertical projections summation of image contents Image rotations by arbitrary angles Image statistics Dark field and flat field corrections Renormalization of an image sequence based on the intensity statistics in a small region of interest ROI e g to c
27. ompensate for a decay in primary intensity Rebinning in 1 2 or 3 dimensions Sharpening and smoothing of images Noise reduction 2D peak detection in images Fourier transforms of images in 2 dimensions 1 1 Structure of this manual The remainder of this manual is divided into 4 main chapters Chapter 2 describes how to prepare for the first use of visrock Chapter 3 discusses a first complete round of using visrock from data input to result output It is limited to the absolute essentials and meant to be short and easy to read It should be considered as obligatory reading by every new user of the program Chapter 4 provides guidance to the more advanced features of the visrock program It covers in detail all the available image analysis processing and plotting options and serves as a reference to those users who want to get the most out of the program Finally chapter 5 covers a few very specific functions related to single scientific applica tions It shows how individual task occurring repetitively in some fields of X ray imaging may be carried out by visrock 2 Preconditions to using visrock 2 1 Obtaining visrock The visrock software can be obtained directly from the author based on a personal collaboration agreement 2 2 License policy The visrock software may be used free of cost and for an unlimited time However it must not be redistributed nor made publicly available on the internet on an intranet or on an
28. on ment values The serial version immediately takes the new values into consideration when treating the local environements for the next pixel as it works its way through the entire data array Both variants are rather efficient at eliminating real outliers and only those How ever they are pretty demanding in terms of computing time and particulary working memory Saving of intermediate results will require a maximum of 6 5 times the memory space occupied by the original image data As an example if you are treating an image 28 Dezinger o o Median x y E zib Apply to all data 3D var filter par 1 var filter par 1 Smooth x fa y fa z p w Rebin Smooth 3D var filter serial Figure 13 Noise reduction options series with 100 MB of data and you don t have at least 650 MB of RAM better don t use this function 4 8 5 3D smoothing A more basic way of 3D noise reduction is realized by the Smooth fields 3 numbers can be entered here which represent the lengths along the 3 coordinate axes of a box around each pixel Values inside this box are averaged and the average value assigned as a new value to the central pixel The result of this function is similar to using the 3D variance filter with a tolerance level of 0 but more efficient in terms of execution time and memory requirements 4 8 6 3D rebinning When the rebin option rather than the smoo
29. on coefficient of 1 00 both indicating identity Note also that unlike the previous figure this distribution is not symmetric 26 xedit_choice Choose a second file O mi x Correlate home luebbert Data 1999 06_99 caf C 0006 edf gz witht 2 homes luebbert Data 1999 06_99 caf C 0006 edf gz w home luebbert Data 1999 06_99 caf C 0007 edf gz w home luebbert Data 1999 06_99 caf C 0008 edf gz w home luebbert Data 1999 06_99 caf C 0009 edf gz Figure 11 File selection widget allowing to select a second image with which the one presently displayed is to be correlated the order of seconds To accelerate the procedure the median filtering can alternatively be applied to the original image data by pressing the Apply to all data button after entering the appropriate box width values Be aware that this operation is irreversible unless you are willing to read all the images again from hard disk 4 8 2 3D median filtering When using Apply to all data for median filtering of the original image data an additional and independent box width can be entered into the field labeled z When a value gt 2 is entered an additional 1D median filtering operation will be applied to the pixel value array along the z direction the rocking curve at each 2D pixel location This operation relates the values in adjacent images to each other unlike the 2D filtering operation that is applied to ea
30. opment no documentation yet Don t use FWHM For each pixel calculate the full width at half maximum of the main peak in the local intensity curve FW_percent_M For each pixel calculate the full width at 1 of peak height with selectable percentage x For x 50 the result is identical to FWHM Sometimes more representative than the FWHM map in case of multiple peaks or peaks with broad tails ratio FWHM FW_percent_M Quotient of the latter two quantities Sometimes use ful to detect regions with different numbers of peaks overlapping grains in RCI TI integr d restricted range Summation of intensity across a restricted range of image numbers only rather than the entire series Will ask for numbers of first and last image Useful when multiple peaks exist for each pixel maximum restricted range Similarly for maximum intensity maxpos restricted range Similarly for position of maximum FWHM restricted range Similarly for peak FWHM Angular center of mass For each pixel calculate the center of mass of the associated intensity distribution as a function of angle or image number the w distribution Result is in units of angle Alternative to maxpos statistically more robust The resulting angle is slightly less sensitive to noise than maxpos 12 Angular standard deviation For each pixel calculate the standard deviation of the local I w distribution Result is in units of angles and is a measure of peak width It i
31. overlay the experimental images with resolution rings These are circles around the primary beam spot labeled with the value of their associated reciprocal space resolution in A71 To activate the display of resolution rings in visrock simply press the button labeled show resolution rings In order to obtain reasonable results you should additionally define the appropriate scattering parameters by using the function Edit resolution ring paramters from the Extra functions menu This will open up an extra window see Fig 15 allowing to define the following values ORIG_X ORIG_Y Location of the primary beam spot in the image in pixel units WAVELENGTH X ray wavelength used for recording the scattering pattern in A DISTANCE_MM Distance from sample to camera in mm PIXEL_SIZE_MM Size of one detector pixel in mm 5 5 Functions for Detector Calibration Linear fitting residual dark field slope sensitivity CHI linearity stddev repro ducibility noise Various types of X ray cameras differ from each other not only in terms of pixel size data format and readout speed but also in terms of dark current sensitivity uniformity linearity and noise The latter group of parameters can be determined experimentally from 35 XSCRMENU Figure 15 Defining parameters for resolution ring display a series of pictures recorded with the camera in question either under constant conditions or with vari
32. p wade a A tr ai 4 9 Image processing options sharpening smoothing and peak detection or w XA JDOODOO Using visrock III Special functions for specific applications 5 1 Functions for Rocking Curve Imaging ea ea ee de eS 5 2 Functions for Tomography e nte as as a e ek 8 5 3 Functions for Fin Slicing ls e a ee Sey ee ee Ea n 5 4 Functions for Small angle scattering and general Crystallography 5 5 Functions for Detector Calibration ais are dk beck Be wee BAA Planned future developments of visrock List of known bugs 7 1 Bugs 7 2 Not bugs features Impressum Literature references 32 32 33 34 35 35 38 39 39 39 41 42 1 Introduction what the visrock program can be used for The visrock program was written to facilitate the interactive handling and analysis of dig ital X ray images It was originally developed for applications in Rocking Curve Imaging but was later extended to several other fields of X ray imaging It can be useful in various applications that are based on linear sequences of 2D images sequential imaging Rocking Curve Imaging RCI Visualizing the spatial distribution of mosaicity and lattice quality by a series of plane wave X ray diffraction topographs recorded along the rocking curve of a single crystal LBH00 MLK03 X ray tomography 3D image reconstruction from a series of projection radiographs Her80 visrock cannot do the reconstruction but
33. pplication to an image series the image number is regarded as the component index of the data vector and each pixel as an independent measure of the same vectorial quantity The coordinate transformation creates a new set of images the first of which has a maximum of contrast whereas the last ones are rather flat This algorithm is a rather efficient method for contrast enhancement but somehow dissatisfactory for quantitative imaging in the sense that the intensity values of the resulting images do not have any clearly defined unit 3 3 Saving the results to disk 3 3 1 Postscript output As soon as satisfactory plots of the relevant quantities have been obtained in the two plot areas in the visrock GUI the images can be output almost identically to postscript files To that end click the Map gt ps and or Curve gt ps buttons in the top row of the visrock GUI A default filename wil be suggested containing quite detailed information on the kind of plot The type of postscript plot encapsulated yes no will be adapted to the final filename chosen ps or eps On appropriate operating systems Linux UNIX the newly created postscript file will be opened in ghostview for immediate checking printing 3 3 2 Data output The results displayed in the plotting areas may as well be saved as raw data for later display with other programs than visrock To that end click the Map gt img and or Cu
34. projections from the 3D data block that resides in the program s memory A large number of options is available as can be seen from the list below The first three options represent sections from the original data whereas all the remaining options represent composite images generated from the entire stack of data mostly by projection along the third angular dimension x y Single images Show one of the original images Its number is selectable via the slider at the bottom of the GUI x z x omega Show a section from the 3D data block perpendicular to the original image planes This is a sinogram in the case of tomography with vertical rotation axis along y 11 y z y omega Show a section from the 3D data block perpendicular to the original image planes This is a sinogram in the case of tomography with vertical rotation axis along zx integrated Intensity For each pixel show the sum of intensities across the entire image stack maximum Intensity For each pixel show the maximum intensity reached anywhere across the entire image series maxpos For each pixel show the angular position or image number where the miaxi mum is reached minimum Intensity For each pixel show the minimum of intensity reached anywhere across the image series Rarely used sometimes useful with tomography images minpos For each pixel show the angular position or image number where the minimum is reached Int_and_Pos Under devel
35. rkaround is to select large series not manually but via a text file containing the names of the image files via the Read file list button Program stops while reading image series The problem is currently under study A workaround is not to touch the entire computer during reading in particular don t change between windows or virtual desktops Histogram display won t work or percentile ranges are not translated into absolute disp In both cases the histogram of map values cannot be calculated correctly by IDL This problem is related to some IDL internal functions The reason for this failure is currently under study Solved with version of September 2004 no longer a problem Program stops while producing an output file postscript Sometimes visrock stops working while writing a result image to postscript file or most often while opening the postscript file for display on screen using ghostview This is not really IDL crashing but rather the gv child process that does not terminate Unfortunately the child process cannot be terminated externally and IDL cannot be told to not wait for it either The only solution kill the entire IDL process and start again To avoid this kind of crash be a little patient Take half a second between consecutive mouse clicks and give the program time to digest your requests This clearly helps to minimize problems of this kind 7 2 Not bugs features In some cases please no
36. rm data can be displayed in the map plotting area Fourier data are complex numbers so the user can choose to plot the real or imaginary part or their absolute values This choice is made via a droplist on the right of the map plotting options see Fig 5 TODO Fourier droplist abbilden 2Note that when any one of these two buttons is active value and profile extraction from the map by mouse clicking will not work at least in the present version of visrock 21 4 5 Histogram display TEx Quit Histogram Save this plot Save these data 2 Real data w Fourier data 3 xlog F FUHH mint 1 000 maxt 19 000 Transfer to xplot Frequency of occurrence 0 000 0 001 0 002 0 003 0 004 0 005 Pixel value Figure 7 Histogram display The Show histogram button see Fig 1 allows to display a statistic of pixel values and their frequency of occurrence in the current image i e a histogram of pixel values in the plotting area The histogram is taken only over the currently zoomed region and thus changes with the zoom state center and magnification factor A separate window see Fig 7 containing the histogram plot will be opened which can be kept open for later use if required since it does not block action in the main window A few buttons allow to manipulate the histogram plot Save this plot Output the plot to a postscript file A default filename of tmp ps will be suggested but can be changed
37. rotation axes and or detectors may may prevent successful reconstruction unless it is diagnosed and documented 5 2 1 Flat field calibration A flat field correction can be performed automatically similarly to the case of dark field correction described above The name of one or several primary beam images must be entered into the field labeled Prim beam before reading the main series of images After reading and possibly dark field correction the experimental images will then be divided by the primary beam data Note that this entails a change of data type which in many cases means increased memory requirements e g changing from unsigned short to float means a doubling of RAM space 33 5 2 2 Correction for primary beam decay At most synchrotron sources the primary beam intensity slowly decays between injections To correct for this decay in the series of projection images proceed as follows Select an area in the images which is illuminated by the beam but never sees the sample This can most easily be verified by switching to minimum Intensity analysis mode Zoom to exactly this area and switch to ROI Integral curve analysis option If the curve displayed in the curve drawing area is rougly constant no correction is necessary Otherwise use Normalize to ROI as background function in the extra functions droplist to correct the entire set of images for the visible decay After this the curve on display sho
38. rrelation coefficients between pairs of images from a series of 10 primary beam images Both the x and the y axis are in terms of image numbers defined from 0 to N 1 Note that the distribution is symmetric and that values on the diagonal are equal to 1 00 simply indicating that each image is identical to itself The non diagonal values show that images nr 0 7 are rather similar to each other whereas images 8 and 9 deviate more strongly The 2x2 fields in the upper right corner show that these last 2 images are again rather similar to each other In summary beam conditions stayed constant until image nr 7 after which an unknown sudden slight change occurred The nature of this change may be further elucidated by other functions of the visrock program As an example the correlation function between e g images 6 and 8 may give hints whether a lateral or vertical shift of beam or camera gave rise to the change 25 R values of pairs of images 0 000 0 04250 0 08499 0 1275 0 1700 0 2125 0 2550 0 2975 0 3400 0 3825 0 4250 0 4675 Image nr TERE EEEEES O 2 4 6 3 10 Image nr Quit EN proj_x proj_u extra Wzlog 4 lines 1 auto_levels J points int_points JW ylog F fill F leg 1 bw I xlog Figure 10 Map of spatial R values between pairs of images from a series of 12 dark field images Note again that values on the diagonal are trivial with an R value of 0 00 being equivalent to a correlati
39. rve gt x dat buttons in the top row of the visrock GUI Maps can be stored in almost any of the image formats discussed in section 3 1 3 Curves will be saved as ascii files with two data columns and one row for each image in the series 14 3 4 Terminating the program When your work is done terminate the program by clicking either the Quit or the Exit button in the upper left of the visrock GUI The former will close the GUI but leave the IDL session open with the values of various variables still in memory The latter will close the IDL program as well and exit to the Linux shell Windows desktop 15 4 Using visrock IJ Advanced functionality for ex perienced users 4 1 Curve analysis options When the user clicks on a pixel in the map plotting area a curve plot intensity versus angle image number will be displayed in the second right plotting area The scaling of the x axis of the curve can be selected via the Delta omega input field in the top row of the visrock GUI If a value of 1 is entered the x axis can be interpreted as image numbers if the angular increment used in the scan is entered the x axis can be interpreted as angles The Start omega input field can be used to select an angular offset i e a shift of the entire x axis The exact meaning of the y axis of the curve depends on the setting of the option selected in the curve analysis droplist just below the plot The following functions are
40. s a statistically more robust alternative to FWHM which may be preferable in case of noisy data multiple peaks and or peaks with broad tails N_peaks Calculate the number of peaks in each local intensity curve Calculation based on the algorithm described in Sil96 Average For each pixel calculate the average intensity across the image series Median For each pixel calculate the median intensity across the image series max min For each pixel calculate the difference between maximum and minimum in tensity across the image series Sometimes useful for tomography data Standard deviation For each pixel calculate the standard deviation of the associated vector of intensity values Result is in terms of intensities High values indicate that something changes somewhere in the entire series I over sigma Ratio of average intensity over intensity standard deviation for each pixel noise lt gt Poissonian Intensity standard deviation divided by square root of average intensity for each pixel Useful when evaluating the homogeneity of a series of flat field images wafer_present_yes_no Binary image yes no indicating which pixels looked on diffract ing material yes or air no Calculation based on selectable upper lower limits for FWHM and max_Int Must have been calculated before using the mask wafer area button located on the right side of the visrock GUI threshold Binary image yes no showing where maximum In
41. te that It s not a bug it s a feature Known restrictions of this kind are e There is no way to stop a running movie once you have started it you must watch it till the end If you want to save time switch to linear non log mode e Line extraction from maps does not work when the invert x y buttons are active e Line extraction does not work when using physical length scales for the x y axes rather than pixel numbers 39 e It is not possible to add new images to a series already in memory Rather one has to read the entire series again e There is no way to output a series of images as a movie mpg or avi format for example Although this is theoretically very easy in IDL it requires a special license An alternative Movie creation is very simple on Linux using the tools from the ImageMagick suite convert in conjunction with zimg for initial conversion from edf to other formats Generally please be aware that this program was written by a single scientist not a group of professional programmers The focus is on some advanced data processing functions and innovative scientific applications not on extreme user friendliness routine application and ultimate stability Therefore it may happen that the program behave in unforeseen ways or even crashes Watch the IDL output window on Linux this is identical to the terminal window from which you started visrock Some program errors cause error
42. tead of a single dark field file the user can alternatively specify a set of N dark field files simultaneously e g by holding the SHIFT and or CTRL buttons pressed while selecting files These will be understood as several noisy instances of the same basic image and will be merged into a single denoisified dark field using the Dezingering algorithm described in section 4 8 3 5 1 2 Masking sample areas In Rocking Curve Imaging the diffracting sample areas often cover only part of the camera s field of view The non diffracting parts appear very noisy particularly in the position of maximum and FWHM maps since the analysis is carried out on spurious peaks To mask out these areas i e plot them in the background colour the Mask wafer area can be used In order for this to work the wafer_present_yes_no analysis option must have been selected first This will carry out an analysis of each local rocking curve and decide whether it corresponds to diffracting material based on two criteria maximum Intensity and FWHM These two quantities must lie between respective minimum and maximum values which can be entered interactively As a result a binary map 1 diffracting 0 non diffracting of the sample area will be displayed 32 The limiting values can optionally be changed and analysis repeated e g by pressing the replot button until the binary image matches expectations When this is the case these
43. tensity exceeded a se lectable threshold Gauss_fit max_Int Apply Gaussian fit to highest peak in each pixel s intensity dis tribution and display the peak height of the fitted curve Robust alternative to max_Int less sensitive to noise Gauss_fit max_Pos Similarly display angular peak position of fitted curve Gauss_fit FWHM Similarly display half width of fitted curve Very interesting alter native to FWHM less sensitive to noise and less prone to errors due to discrete scan step width Linear fit Background Apply linear fit to local intensity distribution and display residual fitted intensity for w 0 Useful mainly for detector calibration purposes Linear fit Slope Similarly display slope of linear curve 13 Linear fit Chi Display chi square for local fit High values indicate deviations from linear local curve shape Linear fit Status Check result of local fit 0 for success 1 for error 2 for inaccurate result 3D Intensity Display the entire 3D data block similarly to volume data in tomography 3D Peak locations Undocumented feature Principal components Apply principal components analysis to the image stack This is a standard procedure in multivariate multi dimensional statistics A new rotated coordinate system is introduced in such a way that the first components of the new data vectors contain a maximum of the total variance of the data and the last component a minimum For a
44. th option is selected the same smoothing mechanism will result in a new data block with reduced dimensions i e smaller numbers of pixels along the three axes by factors corresponding to the values entered into the three fields Note that these last two functions are irreversible unless you are willing to read the original images again from hard disk 4 9 Image processing options sharpening smoothing and peak detection visrock can perform a number of image processing options on the data to be displayed in the map plotting area Original data No image processing operation Deriv_x Show discrete derivative of image data along the horizontal axis instead of the original image In other words replace pixel value u j by Oru Uii j Ui j Deriv_y Similarly for the vertical direction Modulus of Gradient Absolute value of the 2D vector constructed from the two deriva tives e 4 0 u 0 u Good for detecting areas of fast changes in image contents Phase of Gradient Direction of the same vector in 0 27 Often not very useful 29 Laplace 1 Convolution of original image with a 3x3 kernel given by 0 1 0 1 4 1 0 1 0 Good for detecting local peaks in the image Laplace 2 Convolution of original image with a 3x3 kernel given by 1 1 1 8 Al 1 1 1 Also good for detecting local peaks in the image Laplace 3 Convolution of original image with a 3x3 kernel given b
45. tions 4 2 1 Plot range selection The button labeled 1og allows to change back and forth between linear and logarithmic intensity scale The button labeled Full range determines the range of values shown on the y in tensity axis When the button is not pressed the y range is individually adapted to the actual curve thus maximizing the visible contrast When the button is pressed the y range is determined from the minimum and maximum values in the entire 3D data block This facilitates the comparison on an absolute scale of several different extracted curves obtained by clicking in sequence on different pixels in the map 4 2 2 Peak detection The button show peaks when pressed will activate auomatic peak detection in the current curve Real peaks as opposed to local absolute maxima will be marked by a sign This serves mainly as a control mechanism for the N_peaks analysis option in map display Peak detection is based on a curve sharpening algorithm see Sil96 followed by a search for local maxima in the sharpened curve Maxima must be higher than adjacent minima by a factor that can be regulated via the peak_detect max_ratio input field The sharpened curve as an intermediate step towards peak detection can additionally be displayed by pressing the show sharp button 17 4 2 3 Curve shape analysis Curve shapes can be analyzed either by a phenomenological determination of half widh
46. ts button FWHM or by fitting with a linear button Lin Fit or Gaussian button Gauss Fit model In all three cases the resulting parameters will be displayed in a corner of the plot 4 2 4 Noise reduction The median filter button will apply a one dimensional median filter to the current extracted curve This will smoothen local spikes and reduced noise but also flatten real peaks and slightly reduce resolution along the x direction The width of the filter window can be regulated via the smooth median width input field The Dezinger button will try to reduce noise from extreme intensity values in in dividual positions zingers by applying a statistical criterion BTG99 This is mainly meant as a control facility for the Dezinger option in map plotting which works according to the same algorithm 4 2 5 Other plot options Pressing the oplot button allows to plot a new curve without erasing the old one This facilitates comparison of curves extracted from several different pixels When the VBar button is activated a vertical red line in the curve plot indicates the angular position image number in the series at which the picture presently displayed in the map plot area was taken 4 3 Image Plotting options 4 4 Axis units The x and y axes in the map display can be labeled by physical units rather than pixel numbers To this end select Edit plot options from the Extr
47. uld be exactly horizontal 5 2 3 Sinogram display Sinograms can be displayed by using the x w image display mode for vertical rotation axis or y w mode in the case of a horizontal rotation axis Starting from an individual projection image click anywhere into the image with the left mouse button This will have the effect of fixing the y position for x w mode or the x position for y w mode at which the sinogram is to be taken Then switch to the appropriate image analysis mode Note that in these modes the image number slider at the bottom of the visrock GUI will change values and function now allowing to switch to different x or y positions sinogram numbers 5 2 4 Finding the location of the rotation axis To find the location in pixel units of the rotation axis horizontal or vertical in a stack of tomographic projections proceed as follows In sinogram display identify one strongly absorbing feature Take the average between the x or y positions at w 0 and w 180 5 2 5 Zero padding In case the illuminated area in the experimental projections is not symmetrical around the newly found rotation axis the image area can be extended by filling with zeroes in logarithmic absorption mode or equivalently ones in transmission mode TODO Explain how 5 2 6 Detecting axis wobble TODO Discuss the extra functions in curve analysis expert features 5 3 Functions for Fine Slicing The Fine Slicin
48. y T 28 E 2 4 2 D 2 4 A third way of detecting local peaks in the image For details on the relevant differences between the three see e g Pra91 Peaks Smooth Laplacel First smooth image by a median filter of a given width then perform peak detection as in Laplace 1 Good for distinguishing noisy and spurious local peaks which will be levelled out by the smoothing operation from real ones mean local Convolution of original image with a 3x3 kernel given by r d 1 S400 1 8111 Replaces each pixel by the average value of its 8 nearest neighbours Good for image smoothing and as a preparation for the signal mean local operation signal mean local Similar but additionally subtracting the value of the central pixel itself Good for detecting prominent pixels that are very different from their local surroundings stddev local For each pixel calculate the standard deviation of values of the 8 nearest neighbours again by convolution Good for detecting areas of strong local changes and as a preparation for SNR local 30 SNR local For each pixel calculate the local signal to noise ratio by dividing signal mean local by stddev local Helps to identify real local peaks in noisy images by showing which pixels exceed their surroundings by more than the local noise level This list is of course very incomplete compared to the many miraculous procedures contained in books like J h02
49. y other publicly available storage space The author will be happy to receive suggestions for new collaborators and users of the visrock project 2 3 System requirements 2 3 1 Software requirements visrock was written in the IDL programming language see http www rsinc com The software is distributed as an IDL sav file which requires a working IDL installation in order to be run Ideally the user s institution should have an IDL license which is the case at almost all synchrotrons many universities and other research institutions However from IDL version 6 0 on sav files can also be run from unlicensed IDL installations the so called IDL Virtual Machine By default visrock is optimized for the latest version of IDL version 6 0 as of July 2004 2 3 2 Operating system IDL runs on almost any modern operating system Linux Unix es all kinds of Windows Apple visrock can therefore be run on any type of computer Only some special conveniences realized by calls to external programs are limited to Linux UNIX systems The concerns in particular the input of compressed data and the display on screen of postscript files 2 3 3 Hardware requirements RAM visrock assumes that the entire sequence of images can be loaded into RAM simultaneously This is sometimes a very severe restriction to the allowed number of images and or pixels An example Even for a well equipped computer with 2 GB RAM and for images of
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