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SAXSGUI User Manual v.2.05.02

1. gt Same as last Allows you to quickly apply the same error normalization factor as the previously calibrated image The calibration is lost when MATLAB is closed Compute To compute the Error Normalization Factor use an image which has a large flat region After choosing this menu item you are prompted to define a rectangle The program then calculates the actual error normalization factor based on a calculated mean and observed statistical distribution of pixel values For photon counting detectors gas detectors and Dectris Pilatus detectors detectors the value should be close to 1 Manual Here one can enter the parameter manually Uncalibrate Remove error normalization calibration data from the image What is this Briefly explains what this menu can be used for SAXSGUI User Manual v 2 05 02 15 3 1 5 The Reduction menu Data reduction is crucial to obtaining data that you can fit and model Examples of data reduction are background subtraction flood field correction absorption corrections and absolute scaling Data reduction can be done either directly on the 2D images themselves or on the 1D spectra often obtained by averaging radially or azimuthally See Appendix 2 This menu allows you to specify which reduction parameters are to be applied to the image as well as stating whether you want to see them applied interactively or you can wait till later for example when averaging gt Same as last Allows you to
2. Ideally one must make a flatfield measurement at every detector distance In order to do correction on individual pixels significant statistics must be built up One must remove the beam stop so that it does not block a portion of the beam For these reasons obtaining flatfield data becomes a long tiresome procedure that in practice is rarely done So as a hack to doing this properly we have developed a tool Flatfieldmaker which combines 1 2 3 4 5 Low intensity noisy data from a know flat scaterrer like water High intensity good data from a strong broad scatterer like glassy carbon A mask to tell the tool which areas to consider reliable data and which to consider unreliable A routine to calculate the flatfield intensities in the non masked areas An interpolation routine to guess the flatfield intensities in the masked areas to finally create a complete flatfield which can be used in the reduction of other data Needed Files The files needed for this demo are in the Flatlfieldmaker Data folder They are taken with a 200 mm detector at a distance of roughly 850 mm Here is a brief description Data File 183 184 185 186 187 188 189 Description Transmission Water 0 155162 Buffer 0 190599 2mg BSA 0 147443 20mg BSA 0 144163 Glassy carbon 0 521174 Empty Cap 0 81 Water 0 15 SAXSGUI User Manual v 2 05 02 35 agbehnt Silver Behenate To create the
3. Once the mask has been created you can save the mask as a MATLAB data file and then load it into your application Reservations and Acknowledgements Maskmakergui was created by Karsten Joensen JJ X ray Systems under MATLAB 6 5 and for a long time worked best with this version After some period with idiosynchrasies maskmaker was altered to work with Matlab R2010a 7 10 0 One of the routines employed in Maskmakergui is draggable which is a VERY nice routine created by Francois Bouffard which is available at the MATLAB Central file exchange http www mathworks es matlabcentral fileexchange loadFile do objectId 4179 amp objectT ype FILE SAXSGUI User Manual v 2 05 02 32 Maskmakergui Details Input parameters Maskmakergui takes as its input any 2D data set and plots it in the leftmost window The following sequence of command commands will ensure a 2D saxs image is displayed gt A getsaxs gt Maskmakergui A pixels The first commands allows you to chose a file containing 2D data for SAXS and the second command starts maskmakergui with the pixel values loaded Creating a region To create a region you should first specify the type of region by choosing on the pull down menu displaying rectangle You can choose Rectangle Circle Splice or Polygon the polygon must be convex in order for the region to be defined properly Once you have chosen the type of region you should press create and a yellow informati
4. essentially is a tool for doing primary calibration using water as a a priori standard The tool requires that the active image in SAXSGUI is the image taken of water within a holder and that you also have available an image taken of the holder without water empty El Absolute Calibration by VVater Panel J File Water And Holder Transmission 0 18 Mask Mask File mask_mr_0709 Flatfield holder The tool then requires that you Empty Holder Transmission 0 82 Empty Holder 000116 fill in the panel seen below at least with Dark Current the information on transmissions and ae ies file name When pressing Calculate it will calculate the actual sample thickness and the absolute intensity factor Note This default operation for this tool is at CuKa radiation If other energies are to be used the attenuation length of water should be changed according in the SAXSGUI preferences in the File Menu of the SAXSGUI window gt Absolute Intensity By Glassy Carbon This menu item uses a Glassy Carbon measurement as a secondary intensity standard It assumes that the Glassy Carbon image is the active image in the SAXSGUI window It also assumes that the particular piece of glassy carbon has previously been calibrated for example against water and that the calibration value has been entered into the SAXSGUI preferences gt Absolute Intensity Save Calibration Save the center coordinates in a file so you can l
5. intensity vs momentum transfer for Silver Behenate the plot has 200 linearly distributed points The leftmost peak 1s 10 actually not a peak but rather a result of the beam stop blocking intensity for the smallest momentum transfers l0 x Display PlotType Analysis Export Batch Agbe_Ir 30s 2755 45614 mpa In the top of the figure you ll see several menu items which shall be described in more detail below Note if you desire the standard Matlab figure window menus for example to manipulate the axis in detailed ways you can toggle the Display gt Matlab Menus menu av erage intensity counts per pixel per second 0 aua dap dace a es DA ada US momentum transfer q At 3 2 1 The Display menu The menu allows for rapidly changing the axes between logarithmic and linear scaling as well as toggling error bars on and off There 1s a bit of difference between available features for intensity vs momentum transfer or intensity vs azimuth angle as shown in the table below Availability of axis scaling and I vs momentum transfer plots For Intensity vs azimuth plots plot content The menu also provides a zoom menu item that allows you to zoom in on region of the figure that may interest you 2 2 2 The Plot type menu Many different types of plots have shown their use in SAXS data presentation A couple of these are available under this menu Availability of axis scaling and I v
6. output dir C Data Kavala results 3 if not given the user will be prompted o o oo HHH ll DS o o ot DESCRIPTIONS S335 SSS SSESSESESSESESESEESSESSESESES This file contains the variables required to do various degrees of auto processing in SAXSGUI It can be applied without changes to both single file processing and multiple file processing averaging only for now olo The variables are divided into 2 sections 1 Reduction Info relevant for any particular setup of the existing SAXS instrument Will need to be changed when the setup is changed 2 Reduction parameters that might change for different SAXS systems 3 How to average the data 4 What to do with the averaged data Only gq calibration and centering are absolutely required If other reductions are desired they must be included herein If they are excluded the relevant reduction will not be performed The information in this file complements the information that is saved in the data info files Any information given in the info file always overrides information given in this setup file Presently only the Molmet Rigaku mpa info files are supported O O 6 DO 0 6 0 O 6 0 0 0 0 OO 0 0 0 0 0 O O O 6 O O OO OO O OO O 6 0 O OO OO 6 O DO OO O O OG 0 0 6 6 OO 6 O OO 6 OO DDD DOC DDD GD ic So coco DESCRIPTIONS GG eo DDD DDD CIS DDD DD O o o o o 9 o o o 2 o o o 2 o 2 o o o 2 o o o This file may optionally inc
7. 0 General Introduction 1 1 What this manual does and does not This manuals describes the windows and menus of SAXSGUI in some detail focusing on allowing users of SAXS data to navigate and make informed choices about actions within the program It does not teach or instruct the user on recommended practices for data reduction and analysis 1 2 What SAXSGUI does SAXSGUI reads SAXS images from files allows you to explore the images visually and performs various operations and transformations including full reduction of data as well as some basic fitting both IFT and modeling It also can be used to do some degree of batch processing multiple files SAXSGUI is provided under the GNU public license 1 3 The underlying language MATLAB and SAXS objects We ve built SAXSGUI based on the MATLAB scientific programming language We extended MATLAB with a new class of objects SAXS objects designed to store manipulate and display SAXS images Many of SAXSGUI s capabilities are also available at the MATLAB command line Type ohelp saxs at the MATLAB command line for more information If you want to see what an actual saxs object looks like type gt A getsaxs and you ll get a printing of the SAXS object created from the image file you choose 1 4 Supported MATLAB Versions Version 7 10 0 R2010a SAXSGUI was originally developed for Matlab 6 5 0 R13 which came out in 2002 Since then Matlab has undergone some changes including s
8. Dark count file Comments sample_thickness 0 1 background_transmission 0 15 temperature 30 PhotoDiode 730 632E 12 The comments string should all be on the same long line and enclosed in The parameters are keywords and must be written exactly as seen The order doesn t matter SAXSGUI User Manual v 2 05 02 21 The user can either construct the LabView script so that the comments files are generated by the script or add them at a later time The more general parameters for the reduction are provided in an Auto Processing configuration file as seen here o See full description at bottom of file SReduction Info if it has a value it will be included in the reduction matlab center file C Data Kavala center mr SREQUIRED must be created in SAXSGUI matlab calib file C Data Kavala qcalib mr REQUIRED must be created in SAXSGUI sflatfield filename C Data Fe55FloodField 1 2 4 40kV_1 5kV_11 15V mpa abs int fact 37 6 mask filename C Data Kavala mask ads empty filename C Data Kavala empty mpa should be included in the info file o empty transfact 0 1027 should be included in the info file ssolvent filename C 000066 mpa should be included in the info file ssolvent transfact 0 23 should Be included in the i nfo file ssolvent thickness 0 104 should be included in the info file o Generic Info error _calib 1 z should be 1 for Molmet gas detectors sdarkcurrent filename C Data 000067
9. End el E id a The menu item invokes a Bayesian A i YO Fe e Inverse Fourier Transformation sou Fo fit e program called BIFT The program fal PEE 4 is based on a Bayesian approach to a EO VN IFT of SAXS data first described oa or oe or On Ui UE Us Es EE NE E by S Hansen novv at the a E stg ec lpi pot University of Copenhagen Life de mm H Sciences Department BIFT has a been coded by K Joensen JJ X je y 4 Ray Systems ApS and the user is a z bid referred to BIFT program manual alau el supplied separately SAXSGUI User Manual v 2 05 02 21 3 2 4 The Export menu The data in the plot window SAXS data can be saved in a couple of formats e Comma separated dataformat csv with no header lines e As PHD files Glatter format e As Rad files Risg format Only one curve can be saved to each file In the future there may be several options for exporting format but presently all data from a single plot are exported to a single file in X Y AY in 3 columns 3 2 5 The Batch Processing menu SAXS data may at times consist of a whole series of images all to be reduced in the same way SAXSGUI currently provides 2 ways to approach this The first is the interactive Batch processing by Graphical User Interface template based way which allows you to reduce a large number of files in the exact same way you have done for the curve in the figure window The secon
10. Pixel 150 Mask azimuth degrees Flatfield Correction Empty Holder Subtraction Dark Current Subtraction 100 Readout Noise Subtraction Sample Transmission Absolute Intensity 50 Ca co Sample Thickness Zinger Remova 005 01 O15 02 O25 03 0 35 momentum transfer AT SAXSGUI User Manual v 2 05 02 17 To perform the averaging and obtain the data in plotted format you can either press the New plot button to obtain a new figure window or the Add plot to add the result to the last visited plot window Known Bugs 1 As seen in the above screen dump you can choose reduction type even though no reductions have been specified previously in the reduction panel Solution These should be disabled Severity cosmetic gt AutoProcess The previous menus are all very useful when you are operating in a very interactive mode calibrating centering etc etc But if you are taking many SAXS images with very similar parameters requiring very similar processing and similar outputs then perhaps it is time to consider auto processing Also if you are used to working with batch files and configurations files the autoprocessing may appeal to you more than the GUI approach The present version of the Auto Processing only works for Molmet Rigaku data mpa format that has been taken with LabView SAXS control program with some care taken to get the right information into the info file Other users can contact JJ X R
11. causing a few strong localized spot in the images These are typically called zingers The electronics on each pixel is very delicate and pixels may in some limited amount develop into bad pixels over time These can either go dead or start firing rapidly Most bad pixels are flagged as such during manufacture and testing but others may develop There are routines in the Dectris software to handle this however one may experience such bad pixel until the correction routines in the Dectris software are alerted to this The basic solid plates can be placed only some millimeters apart creating a 17 pixels wide dark band in the image For simple averaging with no mask this would create havoc on our averaged data To address these three issues hopefully making the interactive reduction simpler we have 1 2 3 Created a zinger removal routine in the SAXSGUI Alter Clean up This looks for zingers in the image and creates a region of NaN in the immediate vicinity of the zinger Pixel with NaN values are ignored in the averaging routines Created a bad pixel remover in the SAXSGUI Alter Clean up routine This looks for single pixels with very intensities and creates a small region of NaN just around this pixel Once cleaned up the color scaling is adjusted to the new value range When loading a tiff file whose header files have the string PILATUS 300K inside the loading program automatically fills the dark b
12. mpa snormally so low not required sreadoutnoise filename C Data 000068 mpa snot required for Molmet detectors zinger removal 0 snot required for Molmet detectors sAveraging Info This section is optional Comment out to stop before averaging do average 1 l do averaging O do not do averaging I vs q 1 l do I vs q O do I vs phi Default is I vs q phistart 0 sazimuthal start angle in degrees phiend 360 azimuthal end angle in degrees qstart 0 001 radial start value qend 0 35 radial end value xaxis type lin can be lin or log num xpoints 400 reduction type s reductiom text 1 number of points on the x axis can be default s spectra by sprectra or p pixel by pixel 1 means include reduction text 0 means do not include Output Info This section is optional Comment out to stop at 1D plot figure window do output 1 value 1 means output is desired value 0 no output olo new 1 l plots in new window O plots in existing window print 0 l print result on the printer print1D2jpeg 1 l save 1D figure in a jpeg file sprint2D2jpeg l save2fig 0 Il oo l save 2D saxsgui window in a jpeg file Does not work nicely save figure to matlab figure file save2columns 0 Saves data in commaseparated variable g phi I O does not save save3columns 1 Saves data in comma separated variable q phi I dI O does not savea addon name kj saved files have these additional extensions o
13. of centering and q calibration partial rings offsets etc 2 Mysa Calibrator Ver 18 04 2008 Beta JE File Edit View Insert Tools Desktop Window Help Detector Dist mn Press End to proceed or start again gt Q Calibration Save Calibration Save the calibration values in a file This is necessary if you want to use the file based auto processing feature but also useful if you want to revisit the dataset gt Q Calibration Load Calibration Load the calibration values from a previously saved calibration file gt Q Calibration Uncalibrate Remove calibration data from the image Display in pixel coordinates again SAXSGUI User Manual v 2 05 02 12 gt Center This menu item allows you to select the center in one of may ways Once you have specified the center for the SAXS image SAXSGUI displays a lower resolution polar transformation in the right side of the SAXSGUI window using the same color mapping as the original image gt Center Same as Last A quick press menu for using the last center calibration Tip Start your session by calibrating with a sample with a well defined center for example Silver Behenate Sample and then use this Same as Last menu on the following images Center Auto Compute Center This unique little feature calculates the best fit center based on quick optimization routine Most of the time it does a very good job Simply activate the menu Tip If this routin
14. the regions are referred to as RONI s short for Regions of Non Interest since the program actually determines the mask as the inverse of the Union of all the regions that you don t want or of all your Regions of Non Interest SAXSGUI User Manual v 2 05 02 33 Creating many regions You can create up to ten regions and have complete freedom over which regions you want to apply in the mask creation and which you want to ignore using the active checkbox Saving the regions Now that you ve put all this work into defining your regions it is a good idea to save the information on the regions this is not saving the mask only the regions So do this by pressing the Save RONI s button Loading the regions If you have previously saved a set of regions you can load these regions by using the Load RONI s button This is a useful feature since most of your masks will have the same number of regions that may just need to be adjusted slightly So in this case load in the regions adjust the positions and the size and create the new mask Creating the mask Since there are a lot of buttons in the panel one should first create the mask by pressing the create mask button At this stage the display shows the original image with the mask applied The auto scaling is shown so that anywhere there is a good non zero value pixel is red As a result one clearly sees the outline of the mask
15. 0158 Dark Current Ename Browse High Intensity Image 000187 Center File ficenter SAXSGUI User Manual v 2 05 02 37 5 Press make and off you go First you get some messages in the Flatfield parameter window as it reduces your low intensity images and tries to obtain a smooth fit to your averaged low intensity data The result is plotted for your viewing pleasure El Figure 2 File Edit View Insert Tools Desktop Window Help Uchd AAVDEZ A2 0H aD fit to low intensity flatfield data intensity a u S 100 200 300 400 500 pixels from image center 6 onstruct the 2D flatfield image And tells you so mamy And even gives you a status bar El 40 2 min 4 sec remaining SAXSGUI User Manual v 2 05 02 38 8 Once done it displays the constructed flatfield image File Edit View Insert Tools Desktop Window Help JO6eS k XAG0eK a 08 an Constructed flatfield image 1000 900 a00 rog 600 500 400 300 200 100 agg 1000 In addition to the lower intensities toward the edges one sees the characteristic line patterns from wire detectors as well as to regions with reduced efficiency on the detector in two areas at 11 o clock and 3 o clock One also sees that there is a problem near the lower left corner in that the procedure for filling in does not go all the way to the edge of the circular part of the mask A minor improvement of the filling routine migh
16. Deleting the mask If you are not happy with the mask you simply press the delete mask button and you are back to where you were before creating the mask Saving the mask If you are happy with the mask you press the save mask button to save the mask as a MATLAB data file Mask data file format Good pixels are indicated by a value of 1 Bad pixels are indicated by a value of 0 These values are stored in a variable called mask And so if a mask has been saved to the file mask2 mat the command gt load mask2 will create a new variable mask in the MATLAB workspace And gt c load mask2 will put the 2D data in the structure variable c mask SAXSGUI User Manual v 2 05 02 34 Appendix 5 Constructing an artificial Flatfield Objective The objective of this demo is show how to create an artificial flatfield file for later use in data reduction Background A correct way to obtain a flatfield or floodfield image on a laboratory based SAXS system is to place a radioactive source at the location of the sample and measure the intensity observed on each pixel of the detector However this approach has significant drawbacks in the laboratory setting some of them being 1 2 3 4 5 The intensities of the radioactive sources are low The wavelengths of the available radioactive source seldom match the x ray source used in the system for example 5 9 keV Fe source versus 8 05 keV Cu
17. IFF Ra oor enn ease Reena ee untae ery JPEG PDF or a matlab figure file gt SAXSGUI Preferences T EE Glassy Carbon Standard Crossection Calibrated gt Set SAXSGUI Preferences 0 205 Set the SAXSGUI preferences using the P anel seen to Water Attenuation Length function of x ray wavelength units cm the right The preferences pertain to look up data 0 1008 required for the various auto calibration features the l E auto centering features the default smoothing e es paremeters the default zinger parameters the default averaging parameters and the orientation of read fuji eae Seong ae of roneo box image plates si gt Use Default Preferences iage Sed ee eee 3 gt Close Closes the SAXSGUI window Falp Fontsize T Zinger Size of smoothing box 15 finger Zinger detection threshold Zinger Int Awerage Int B Zinger Zinger mask radius of mask around zinger 3 Averaging default number of points in azimutal average l vs q 200 Averaging default number of points in radial average l ws phi 130 Fuji imagePlate Flip Fuji image 0 0 SAXSGUI User Manual v 2 05 02 9 3 1 2 The View menu This menu affects the way SAXSGUI displays images Most of these commands are toggles which turn certain image viewing features on and off When the feature 1s on a check mark appears beside the command in the menu gt Log intensity toggle Display the common logarithm of intensity values This changes the way colo
18. SAXSGUI User s Guide v2 05 02 A Graphical User Interface for Visualizing Transforming and Reducing SAXS Images as well as Limited Fitting by Rigaku Innovative Technologies Inc and JJ X Ray Systems ApS March 17 2010 PO Geeta LI OU ioiai a a a 2 LF What this manual docs and does not enneren i EE E E RN EE 2 CZ NS ES SS GUIES ai a selpede etennmdtseenstmentmenteddnteimemntttasdnstsi 2 1 3 The underlying language MATLAB and SAXS objects wo ccccccccceeeeeeeeeseeseseeseeeeeesessenesaaaaas 2 1 4 Supported MATLAB Versions Version 7 10 0 R20102 cc ccccsssessesesessessseeeseeceececeeeeeeeeeeeeas 2 1 5 Installing SAXSGUI when you have a MATLAB license 2222222222aaaaaaaaaaaaaanananinenenenenn 2 1 6 Installing SAXSGUI when you do not have a MATLAB license oo cccecccceeeeeeseseseeeeeeseeseens 3 LF Starting and stoppin SAXSGULailtadtntadsmetimnestmtatnmmnn A E A 3 LOSA Gs EE CON aeia e E E E E AEE ESEE 5 2 1 The SAXSGUI Window Controls menus commands sssenesenssenessersseresesesteeseressreeseesseresereseeeses 8 De NAW ERGENE WANG ena EE EOE E O E E 8 WED TNS NV EWIE Menan E E 10 Dl IDE ANC r meN E E else ense ce 11 DN DE CAD OMS CN iaia mens stimstimcondustoltmiastetttameimematsttoumemiessimmadmt 11 DNS CSIR EC QUE OC DU titats denses pleta R 16 PLO Tie QUE Encesa las ev i else 17 2E LENE Process mE MeNe diametre MAPS Err te nee tee een ne Rte emer at Maen Rare Cent 17 DE FEW eN MUO Viccion
19. ands with NaN values such that these bands are omitted from later averaging Therefore one does not have to construct a mask to omit these bands SAXSGUI User Manual v 2 05 02 40
20. are available for download at http www saxsgul com saxsgui_win32_pkg exe http www saxsgul com saxsgui_win64 pkg exe not yet and http www saxsgul com saxsgui lin32 pkg zip not yet There are also manuals available at http www saxsgui com manuals zip and demo data available at http www saxsgul com data1 zip http www saxsgui com data2 zip In windows once you have downloaded the package you can run it and the installation of the necessary components will take place In linus you should unzip the package into the directory you want to run SAXSGUI from and then run the MCRInstaller followed by SAXSGUI The additional files should all be located in the same directory as the saxsgui platform program These are o saxs_preferences txt o saxs_ preferences default txt o standard fitfunctions mat SAXSGUI User Manual v 2 05 02 24 Appendix 2 Reduction Spectra by Spectra or Pixel by Pixel SAXGUI allows you to reduce your averaged data in 2 ways gt Pixel by pixel and gt Spectra by spectra The reduction schemes are graphically represented on the next page for a case where reduction consists of subtracting the signal from an empty sample holder from that of a filled sample holder It is immediately clear that if Reduced 2D data is required for example for 2D modeling then the Pixel by Pixel approach has to be used However if only 1D averaged data is required then the Spectra by Spectra approach can be
21. ari aletes demes editat semi mani N 19 22 The PIG UE NN COM seis ea Et en Dc ta pet ae 19 22 TNE DS DI MC Us entens acrediti acci Disco est 19 DDD EE Pl DECat tie sta ao im ene toca eu momet tec ai 19 220 Th Analy SiS Meni iaio tonta ale a aa sa oo ce A 20 Die LNG EX DOCU deine senta tema Manetes etat 22 222 57 be Batch Processie MEM nai e ea E R ssacauist Scusuammeadonncaadcebsesasnc 22 Appendix 1 Installing and running the SAXSGUI executable 0 0 0 0 ceeeeesssesssnensneseaeeceaeeeeeeeeeeeeseeeeees 24 Appendix 2 Reduction Spectra by Spectra or Pixel by Pixel cccccesesesessssesesesssneaeeeeeeeeeeeeeeeeeeeeeeees 25 Appendix 3 Auto Processing on the Molmet Rigaku SAXS SysteM ccccssseesesesssnsneseseceeeeeeseeeeeeeeees 26 Appendix 3 Auto Processing on the Molmet Rigaku SAXS System cccceseeseeeeeeseseesesesssneaeaeeaeaeaeeeees 21 Appendix 4 Masking With MATLAB MasERmaRCrGUI o o ooo9aaaaaaaaaaaaaaaaaamaninininininneneneniinrini 31 IO GNC ON ee bastante aA ih ea tec cp bac a eee dte lace Eloi a 32 IRCSEry allons and sACKNOW ICO Se mMeNI Se isagmnts mate oients emesa tensmoamuae a E 32 Maskmaker our Donl See oest E E N 33 Appendix 5 Constructing an artificial Flattieldmcieihlh smZmmy mbmmmtmmssenmendmemannsen 35 Appendix 6 Special Considerations for a Pilatus 300K esessessesssensnssssssssssseerrereerreseseessnssssssssessesreerene 40 SAXSGUI User Manual v 2 05 02 1 1
22. atus 100K and 300K have special read in filters to handle the dead stripes on the detector Advanced tip to open a SAXS image that you have created in the MATLAB command window as opposed to an image saved in a file type saxsgui image_name SAXSGUI User Manual v 2 05 02 4 3 0 SAXSGUI windows SAXSGUI interacts with you through several windows for example The SAXSGUI window The Fatpix window The Reduction Parameter window The Data Reduction and Averaging window The Figure windows The Interactive Batch Window The Maskmaker window The Flatfield construction window In the following a brief gallery of these windows will be shown followed by a more detailed presentation of available menus The main SAXSGUI window displays images and controls image visualization and transformation r El saxsgui v2 05 01 Fite View Alter Calibrations Reduction Quik_Enter Processing x Top of color scale mn mm mn ii Ll 0 1 2 3 4 AgBeh_hr2 mpa Polar Transformation 0 25 0 15 azimuth degrees 0 15 0 0 2 0 1 0 0 1 0 2 0 05 01 015 02 025 03 035 ZA momentum transfer A Tip Resize and move the SAXSGUI window to suit your needs Maximize the window size to see the most detail and largest region Use the View Zoom command too but read directions for it elsewhere in this document first aixi The fatpix window shows individual pixel intensities from wherever you click o
23. ay Systems to discuss 1f it is feasible to extend support to other setups The Auto processing requirements are described in greater detail in Appendix 3 however in brief it allows SAXSGUI to access 1 aconfiguration file the AP Setup file with parameters that describe the setup the averaging instructions and the output instructions 2 the info file that is saved when data is saved using the Labview program This info file would need to include information specific to the sample such as sample thickness sample transmission empty holder file empty holder transmission etc and use this information to proceed as far as the instructions indicate The Auto Processing sub menu has the following sub menus gt AP Setup This prompts for a AutoProcesseing configuration file gt AP Single File This will prompt for a single mpa file and perform the data reduction and processing requested in the configuration file The latest saved configuration file is always used If no configuration file is requested this menu will prompt for a configuration file first gt AP Multiple Files This will prompt for a list of mpa files and perform the data reduction and processing requested in the configuration file The latest saved configuration file is always used If no configuration file is requested this menu will prompt for a configuration file first SAXSGUI User Manual v 2 05 02 18 3 2 The Figure Window Here you see the azimuthally averaged
24. cess C Evaluate Expression4 2 Choose the sample Evaluate Expressions transmission Actually the T Tam En hi Ir Output oer Save reduced data to separate files Use xy delta y format P 08 a 7 OMe t a eady C Save 2D images tag 2D C Save reduced data to same file C Use x y format but Wwe just have to figure out C Save 1D figures tag 1 DY Descriptive Tag Reduced how to get it reproducibly into the text field in the panel If you do not care what the sample transmission is leave it at 1 which will of course upset any corrections relying on the correct transmission for example Empty holder subtraction 3 Choose the sample thickness 4 Choose how the x axis of the time series should be constructed a By just incrementing 1 2 3 etc b By using time recorded in the data of the header c By using the time that the data file was saved or altered last SAXSGUI User Manual v 2 05 02 22 The latter may be necessary if particular headers don t carry saved time information as is the case with most tiff files 5 On the bottom you ll see the output options which are d Save the 2D data as jpegs e Save the 1D averaged data as jpegs f Save the reduced data to separate ASCII files comma separated g Save the reduced data to one large ASCII file comma separated h Save x y data or x y A y data If saving ASCII data the reduced data will be saved in a file with a name exactly the same as the or
25. d is the AutoProcessing way which uses reduction information in a batch file and ca be accessed from the main SAXS gui window The Batch Processing menu in the Figure window allows you to start the interactive way or to save a batch file that corresponds to the way the data in the figure was reduced and can thus be used as a starting point for the AutoProcessing gt Save Template AP file This saves a file that can be used either directly as input to the AutoProcessing routines started from the main SAXSGUI window or from altered to correspond to actual alternate Autoprocessings gt Batch by Gui TimeSeries At this time Batch reduction of Time Series 1s available through the Time Batch Time Series Panel Panel 15 x Series sub menu When this sub menu is activated the user is requested to Batch Run Time Series 1 1 1 1 Assumes all files are from the same sample same transmission same thickness Cancel click on the line graph that is going to b e the template for the res t o f the Results saved in files with tags added to the file Default Batch evaluation A panel controlling Input Files choose Fies Sample Transmission 70 Use Incremental time 1 2 3 ete A C Use file d ti input to the Batch routine is then Sample Thickness 1 0 pl eae pec opened see below Special Analysis C Evaluate Expressiont In the panel you can Evaluate Expression2 1 Choose the files you want to a E EES batch pro
26. e is having trouble finding the correct center you may help it by first clicking a center to get an approximate center and then running the routine again Or you may need to change the mask radius in the SAXSGUI preference especially if the central region is very intense and extended However the need for this should be very infrequent Center Compute Center by Allows quasi automatic centering based on images with either a ring a partial ring 4 arcs or 2 arcs Center Direct Beam Centering Some systems will allow the direct beam or an attenuated direct beam to strike the detector without a beam stop and use the resulting image to determine the beam center This menu item established the center position based on a 2 dimensional peak fit to such an image Center Manual Allows you to manually enter the center coordinates Or simply take a look at what coordinates are presently used Center Mysa Calibrator This brings up a calibrator tool contributed by Milos Steinhart in Prague that can be used for both q calibration and centering This tool is described in more detail in the q calibration section of this document Section 2 1 4 Center Enter Coordinates This brings up a small panel that will allow you to enter the center coordinates manually Center Click to center Activating this menu brings up a set of crosshairs When you click on a point in the image the corresponding coordinates are entered as being the center T
27. e the SAXS image with the changes you have made SAXSGUI prompts you for a file location and name SAXSGUI saves the image pixel values as either a MATLAB data file with a MAT file name extension or a tiff file 8 or 16 bit or a text file with ASCII characters When saving as a MATLAB file additional information about the image is also saved In this case you reopen the file later with the Open command to continue where you left off If saved as text data files the following formats can be chosen gt x y left image Export the SAXS image in its x y form not polar transform to a text data file SAXSGUI presents a dialog window where you specify the format of the exported data see below what coordinate range of the image to export and how many digits to print past the decimal point for all numbers After you make selections a file selection window allows you to specify where to place the exported text gt polar right image Same as x y above for the polar transformed image the right hand image in the SAXSGUI window El Export text file Export text Oi x y z triplets XU CEC X range 0 25442 to Y range 0 2739 to 1 x y z table pe Ea oe XC FC 13 201 2 eC Z02 15 202 2 Drag range image parameters and history Number of digits to right of decimal point SAXSGUI User Manual v 2 05 02 8 7 O CES gt Export Window El Input SAXSGUI Preferences Sax Export the whole SAXSGUI window to either a T
28. f the reduction panel one can see 5 configurations which each can store and recall separate sets of reduction parameters gt Clear Parameters Removes all the reduction information from the image gt Apply when averaging 1D This is the default mode where reduction parameters are recorded but not yet applied to the data that is shown in the 2D images This puts the least strain on the computer CPU and graphics card gt Apply interactively 2D The reduction parameters are recorded and applied to the 2D images shown This is necessary if one wishes to do save the reduced 2D data for use in another program gt What is this Briefly explains what this menu can be used for water cap reduction Escriptor DEScription SAXSGUI User Manual v 2 05 02 16 3 1 6 The Quik Enter menu gt As last Essentially performs Error Calib gt Same as last Calibration gt Same as last Center gt Same as last and Reduction gt Same as last one after the other and thus becomes a one button complete data preparation gt What is this Briefly explains what this menu can be used for 3 1 7 The Processing menu Most SAXS data analysis from 2D images will make use of 1D projections of the data Either projection along the momentum transfer axis or the azimuth angle gt Averaging 1D spectra Activating this window brings up the averagex plotting window where you can specify exactly how you want the data averaged and
29. fit the parameters or not The panel layout and default provided models are seen in the figure below Data to fit Fitting of 1D data Beta ver CUsersttarsteriDocumentsiOld comFrom C 0606 Data 4achemiSDS data 4 gBeh hr2 mpa qin 0 0019215 gmax 0 23501 Inci Resolution Show Iterations Choose Fitting Function JJ fractal teixera m JJ cvlinder dilute monodisp m JJ_cylinder_elliptical_dilute_monodisp m JJ_cylinder_elliptical_dilute_monodisp_old m JJ_ellipsoid_dilute_monodisp m JJ elipsoid of rev dilute monodisp m i fractal teixera m JJ inf thin dis dilute monodisp m JJ inf thin rod dilute monodisp m JJ polymers flexible gaussian dilute m JJ spheres dilute monodisp m JJ spheres dilute polydisp SZ m JJ spheres dilute polydisp gaussian m JJ spheres dilute polydisp gaussian not volume vveighted m JJ spheres hard monodisp m JJ spheres sticiyhard monodisp m JJ spherical 2shell dilute monodisp m JJ spherical 3shell dilute monodisp m Guess StartVals itval gt Star JJ spherical shell dilute monodisp m JJ toroid dilute monodisp m Param Start al Lo Residual Function Num of tte Chit Tolerance Tip It can sometimes be difficult to find starting parameters that will result in a reasonable fit To play around you can enter Start values and press the Calculate button to see how the calculated curve compares gt Bayesian IFT CEDA dd Py ay Em Vida Cia Quirina Fcio piy aS AT LE TE EE Metts dl Ay ach Ti ot nar ay al AC
30. flatfield you simply do the following preparations 2 Load the high intensity glassy carbon file Then find and save the center in some file Now you are ready to start the flatfield construction 1 From the Reduction Parameter Panel you can find the File gt Construct Flatfield menu m a a ee Pe 2 Which opens up the following El Flatfieldmaker Parameter Panel Files for Flatfieldmaker Low Intensity FlatField Image Transmission 1 Empty Holder Image Optional Transmission E F fiiename Dark Current filename High Intensity Image Center File SAXSGUI User Manual v 2 05 02 36 3 You can now put in the file names and relevant transmissions a You MUST enter ii A mask file saved using maskmaker The mask should as a minimum mask out areas where you do not trust you low intensity flatfiled image beamstop etc example ffmask mat Regon of Non iresrests EE 8 NE dd ES aaa TT w w w Oe w w w w b Ifyou believe your Low Intensity flatfield data would require subtraction of an empty holder you need to put in the information on the empty holder c Ifyou believe the Darkcurrent significantly contributes to the images low intensity flatfield image and the empty holder image then you need to include this one 4 So finally the panel should look like this Low Intensity FlatField Image Transmission 04 E 000189 Empty Holder Image Optional Transmission 0 85 00
31. ge showing individual pixels and labeling each pixel with its intensity value The fatpix window updates the pixel display whenever you click on the left image in the SAXSGUI window showing pixels in the region of your pointer Enlarge the fatpix window to show more pixels at a time Shrink the fatpix window to make updates speedier Close the fatpix window when you finish with it gt Image history Open a window showing the history of the currently displayed SAXS image Close the history window when you finish with it This history also contains the intensity in the image gt MATLAB menus toggle Add standard MATLAB figure menus to the menu bar Choose this command again to remove the MATLAB menus from the menu bar SAXSGUI User Manual v 2 05 02 10 3 1 3 The Alter menu gt Cle gt an Up Zinger Removal This menu item applies a filter to the 2D data that will remove any part of the image that look like a Zinger A Zinger is usually observed in lengthy exposure with solid state imaging detectors and are caused by cosmic radiation interacting with the detector to create a large localized intensity The characteristics of the generic zingers should be given in the SAXSGUI gui preferences accessible from File menu of the SAXSGUI window The data in the zinger region is tagged as if it were to be masked out in the averaging routines Zinger removal would also remove single madly firing pixels gt Bad Pixel Removal This
32. he user can choose the desired q range and azimuthal range on the image to the right Also the various reduction parameters chosen in the Reduction channel can be toggled on and of Tip Use the same as last buttons to save time Data Keduchon and Averaging Spacy a ragian ty mt Lal Ec Ec when analyzing similar Taletale EDENA genh hr apa Sas en images Also opt whether 5 baies to choose to plot in a new Kea nang ter tags i plot area or on top of the Numer cd Prints 200 last figure window Fit menage PEEnsEy va arith 3eme s EH Reductions and Corachons Reduction Type i Epecirn Ey Serem azimuth degrees 01 015 OF OF OF 035 l momentum bransher art Figure windows display the results of averaging radially or azimuthally Display PlatType n Fupest Tip Use the menus below the Display and Plot Type menu to change the axis scaling and produce standard SAXS plots If more advanced image manipulation is required one can invoke the standard Matlab figure menu by asking for it under the Display menu Tip More than one curve can be plotted on any one graph 0 15 025 momentum transfer q A SAXSGUI User Manual v 2 05 02 6 El batch time Seriei Manet Batch Time Series window is spawned through the figure window s Batch menu and allows one to reduce Batch Run Time Series any number of files identically to the way the plot in eee ee ee the figure window was reduced This wo
33. his feature is best used with an image that is somewhat zoomed or at least fills the whole screen Center Save Center Save the center coordinates in a file so you can load it in later sessions You need to do this if you want to use the file based Auto processing function Center Load Calibration Load center pixel coordinates from a MATLAB data file and apply to the current image The data file may have been created by the save center command or may contain a centered SAXS image saved as a mat file SAXSGUI User Manual v 2 05 02 13 gt Absolute Intensity Calibration The absolute intensity calibration relies on the fact that the difference between the data on absolute scale and relative scale is only a factor of some magnitude SAXSGUI refers to it as the Absolute Intensity Factor and the assumption that the source is stable enough that intensity calibrations established for one image are acceptable for later images In other words the program does not explicitly allow for measurements requiring an intensity monitor However for most laboratory sources this is not a problem and intensity calibrations with a secondary standard like Glassy Carbon can be done frequently gt Absolute Intensity Same as Last A quick press menu for using the last Absolute Intensity Factor gt Absolute Intensity Enter Manually Enter the Absolute Intensity Factor Manually gt Absolute Intensity By water This brings up a small panel which
34. iginal data name only with a tag added You must specify this tag in the Descriptive Tag field 6 Once you have chosen the files the start batch button is enabled and you can start the batch processing by pressing it Advanced Batch Feature The Special Analysis section of the table allows you to enter up to 5 MATLAB expressions which will be evaluated for each data file The expression must be composed of strings that could be recognized by MATLAB as regular MATLAB expressions X and Y are the array variables holding the data from the plot At the end of the batch process the result of any one expression which should always be a single figure will be plotted as function of time and also saved to an ASCII file Examples of expressions could be Example 1 sum Y X gt 0 02 amp X lt 0 48 which calculates the sum of all the plot values where 0 02 lt X lt 0 48 essentially area under the curve Such a function could be used to integrated peak intensity evolved over time Example 2 max Y X gt 0 02 amp X lt 0 48 which calculates the maximum value in the same region as Example SAXSGUI User Manual v 2 05 02 23 Appendix 1 Installing and running the SAXSGUI executable Components The executables are distributed from the www saxsgui com website They are distributed in packages containing the saxsgui program the matlab components and various needed and recommended files The distibutable packages
35. ing of the experiment to the end One could then alter the time slice to look at the intensity before the reaction and after the reaction 3 1 4 The Calibrations menu This menu handles all of the calibrations of the images q calibration centering absolute intensity calibration and even the homegrown error calibration gt Same As Last A quick press menu for doing the exact same calibration as the previous image The calibration is lost when MATLAB is closed gt Q Calibration gt Q Calibration Same as Last A quick press menu for using the last q calibration Tip Start your session by calibrating with a SilverBehenate Sample and then use this Same as Last menu on the following images Q Calibration Using Ag Behenate Quasi automatic q calibration with a Silver Behenate image showing a full ring The user is requested to click on three points on the 1 order ring SAXSGUI then calculates the center and diameter of the ring thereby allowing the calculation of the appropriate q calibration in the x and the y direction Tip If you are doing WAXS you may not have the first order ring SAXSGUI User Manual v 2 05 02 11 in the image In this case you can press on n th order go into manual calibration and change the q value for line to n times the value of the first order n times 0 1076 A gt Q Calibration Using Ag Behenate by partial ring Quasi automatic q calibration as above however this version is used whe
36. l Simplex Optimization The themes and models available are given in the table below Double PearsonVI Peak Spline Bckg average intensity counts per mr per second e absolute intensity factor applied 0 0 05 0 1 0 15 0 2 0 25 momentum transfer q A Fitting Themes Brief description E Fitting Models PeakFit Fits to various type of Gaussian Peak with Linear Slope Background peak models Gaussian Peak with Expon Spline Background Lorentz Peak with Linear Slope Background Lorentz Peak with Expon Spline Background Pearson VII Peak with Linear Slope Background Pearson VII Peak with Expon Spline Background Double Pearson Peak with Expon Background PorodFit Fit Simple Porod Porod Model Models Porod Model with Background Fits to Guinier Model Guinier Model FractalFit Fits to a powerlaw Fractal Dimension Power Law function Fractal Dimension Power Law with background OtherFit Available Combined Guinier Porod Combined Guinier Porod with background SAXSGUI User Manual v 2 05 02 20 gt FullFit This menu item starts up a panel intended for bounded optimization of various standard SAXS related models The models are all provided as MATLAB functions in the saxsgui ff 1d directory they have been adapted from the published articles of Jan Skov Pedersen The program uses a Downhill Simplex optimization routine and requires one to specify starting values and bounds for all parameters as well whether one wants to
37. lude information on o o 2 o o o 2 o o o 2 o 2 o o o 2 o o o 2 o olo SAXSGUI User Manual v 2 05 02 28 As seen the file consists of a number of keywords parameters whose value SAXSGUI can recognize and then act upon Anything behind a is considered a comment If a parameter is commented out it is taken as a signal that the corresponding reduction or action is not desired The file is organized into 4 sections 1 Parameters for reduction that will change for different SAXS setups 2 Parameters for reduction that will be different for different installations only 3 Parameters governing the averaging 4 Parameters governing the output Please note 1 that the first section requires two calibration files created in SAXSGUI 2 that do average must be equal to 1 to do any of the averaging 3 that do output must be equal to 1 to do any of the outputs 4 that some minor checking is done for consistency and bad inputs but rubbish values will most likely create rubbish results Also please note Auto processing updates all parameters in the ss SAXSGUI windows images lasts reductions etc Date Reduction and Aviraging Sperti aragon by misning Let Fight Nofior and Top vsiuae qr dug rae TET piim ins Bray Amn adr Aeh ai Per pa Len DOS If do_average 0 then the Auto Processing finishes up by opening the averagex window mar Hunter of ents 70 C Plot ramaga rimen vp
38. menu applies a filter to the 2D data that will remove any single madly pixel In fact it looks for up to 50 such pixels with excess intensity If such pixels are found they and the nearby pixels are tagged for later masking out Smooth gt Gaussian filter Smooth by applying a Gaussian FIR finite impulse response filter to the image to remove higher frequency features This reduces the noise level of the image enabling easier visualization of image features and possibly better symmetry computations centering elliptical normalization You specify the size of the filter size of convolution box and the standard deviation of the Gaussian curve to use 1 e the standard width of the distribution in pixels Smoothing conserves overall intensity gt Undo smoothing Restore the unsmoothed image SAXSGUI maintains the results of certain interim operations such as background subtraction centering and calibration Rotate gt Specify Rotation Enter the desired anti clockwise rotation in degrees Rotates around the defined center ListMode gt Alter Time Slice MPA files may be recorded in ListMode which is a mode in which the pixel position and time is recorded for each individual photon These files are loaded and displayed with all of the available photons This menu item allows one to create an image with only a subsection of the photons Tip This could be used to look at a complete reaction the listmode recording from the beginn
39. n a Windows PC or a Linux machine using an executable The executable is available on the www saxsgui com website In order to run the executable one needs to download and run the saxsgui distribution package For detailed installation and execution information see Appendix 1 There may be some limited functionality on the executable Please let us know if such is discovered 2 2 Starting and stopping SAXSGUI Start MATLAB first Start SAXSGUI from the MATLAB command window by typing saxsgul and SAXSGUI asks what image file to open Once you select an image SAXSGUI displays it in SAXSGUI s main window Use SAXSGUI menu commands and color scale controls to change the way SAXSGUI displays the image to transform the image and to save or export images Stop SAXSGUI by closing the SAXSGUI windows or by closing the MATLAB command window SAXSGUI User Manual v 2 05 02 3 SAXSGUI can open a number of different file formats including MP A files binary and ASCII MATLAB data files mat files TIFF files including special Pilatus detector tiff files Fuji IMG files which require also a inf file Bruker UNW and GRFM files Hecus CBM files as used at Risoe National Laboratory EDF files Rigaku IMG files RADIA format Rigaku image plates Files from Rigaku are usually in MPA format Fuji IMG files or Rigaku IMG files MAT files must contain a SAXS image saved from SAXSGUI or from the MATLAB command window Tiff files from Pil
40. n the main SAXSGUI image You can invoke it under the SAXSGUI window View menu 0072 e A 0 068 Tip Expand the fatpix window to see more pixels at once 0 066 0 064 0 062 0 076 0 08 0 082 0 084 0 086 0086 0 09 0 092 0 094 SAXSGUI User Manual v 2 05 02 The Reduction Parameter window displays images AA and controls image visualization and transformation Apply Corrections O Sample Transmission 0 105 It is also the window from which maskmaker and can be launched and artificial flatfields created Mask Mask File mask051204 Browse Tip Use the Save and load configuration to Save Flatfield Flatfield File 2 4 40kV_1_5k _11_15V Browse typical reduction parameters so you don t have to enter these every time Empty Holder Transmission 0 76 Empty Holder Cap Ir 36005 2920 4000 3 Browse Dark Current Darkeurrent kile filename Browse Readout Noise Readout Noise File PP90_1003_mr Browse Absolute Int Abs Int Factor 1 Sample Thickness 1 cm Zinger Removal Save and Load Configuration Configuration 1 Configuration 2 Configuration 3 Configuration 4 Configuration 5 water cap reduction Description Description DEScHBiGn Escrita Load Existing Load Existing Load Existing Load Existing Load Existing Save above as Save above as Save above as Save above as Save above as Data Reduction and Averaging Window allows the user to choose how to perform the averaging T
41. n there is only a partial ring available It is less robust than the full ring q calibration above gt Q Calibration Manual Calibration This menu brings up a small input panel where you can put your calibration information One can choose to either use the mode where one has a image with a calibration ring whose pixel diameter one can enter or by system geometry where one enters the pixel sizes in millimeters and the distance from the sample to the detector One choose the method by clicking on the radio buttons at the top El q calibration parameters q Calibration Gi By Standard Sample 1 By System Geometry 1 By Standard Sample Enter the wavelength the q value for your calibration line Enter the values for system geometry and the pixel radius of your calibration line The size of pixel must be calibrated from elsewhere The g offset is usually 0 cl Wavelength 1 5405 Wavelength 1 5405 A Pixel radius x 5 42 pixels Size of pixel x mm Pixel radius CY 105 5237 pixels Size of pixel Y mm q oftset ol a carmem Se Ge rom ge fe gt Q Calibration Mysa Calibrator This brings up a calibrator tool contributed by Milos Steinhart in Prague This tool provides the user with more control of the q calibration and centering The user can choose which regions and which pixel intensity levels to include in the calculation of the best fit calibration rings This tool is therefore helpful in the less straightforward cases
42. oad it in later sessions gt Absolute Intensity Load Calibration Load the Absolute Intensity Factor from a MATLAB data file and apply to the current image The data file may have been created by the Save Calibration menu gt Absolute Intensity Uncalibrate Remove the Absolute Intensity Factor from the data gt Absolute Intensity What s this Brings up a text box with a very brief explanation Save and Load Configuration Configuration 1 Configuration 2 Configuration 3 Configuration 4 Configuration 5 Save above as Save above as Save above as Save above as Save above as SAXSGUI User Manual v 2 05 02 14 gt Error Calibration This menu allows you to apply a normalization factor to the standard deviations calculated by SAXSGUI Since SAXSGUI assumes that your pixel values are in units of photons per pixel as is true with photon counting detectors it calculates the expected errors accordingly However when using CCDs and Image Plates the units are different and the calculated errors are consequently completely wrong In order to obtain correct error estimates one therefore needs to apply a correction which we assume to be a simple factor The Error Normalization Factor While it is possible to calculate the correction from detector specifications the SAXSGUI approach relies on computing the Error Normalization Factor from the observable statistics in an actual image ideally a flat field image
43. of Auto processing mode SAXSGUI User Manual v 2 05 02 30 Appendix 4 Masking With MATLAB MaskmakerGUI r El maskmakergui 3 s Region of Non jInterests Exclude Exterior Type of RONI Number Rectangle v I Circle 4 m m a Q a LoadRONIS RONIs Save RONIs 200 300 400 500 600 700 a00 s00 1000 m El maskmakergui Region of Non jInterests Exclude Exterior Type of RONI Number Active Rectangle Cc rcle LE SAXSGUI User Manual v 2 05 02 31 Introduction Maskmakergui is a stand alone MATLAB application toolbox which allows you to create a mask for ignoring bad data pixels in 2D image data It can be called either directly from the MATLAB prompt gt Maskmakergui or from inside MATLAB applications such as SAXSGUI under the 1D and 2D reduction menus Maskmaker allows you interactively define create edit and save up to 10 different geometrical regions rectangles circles slices and convex polygons Recent versions of maskmaker allow you to zoom in to edit or drag the regions however all regions must be created in an un zoomed window For each region you decide whether you want include or exclude the points on the outside Once you have created your regions you can save them and then load them at a later time Once you are happy with your regions you can create a mask which 1s defined as the intersection of all the included points
44. ome very fundamental ones We have struggled to keep the code backwards compatible but have from 2010 decided to support only the R2010a 7 10 0 Since the program is available both as source code for users with matlab licenses and compile code for users with no matlab license we believe this is acceptable We believe that the code is indeed backward compatible till version 2008a 7 6 0 1 5 Acknowledgements SAXSGUI is in its present form mostly the result of efforts by JJ X Ray Systems ApS and Rigaku IT Inc to provide an interactive software suite that was simple to start working with yet had all the necessary and correct has developed since 2002 with input from many users Since its conception in 2001 the following people have contributed to the development of SAXSGUI either through contributons of algoritms source code or good ideas Some of these people were paid most were underpaid and many completely unpaid Scott Barton now Molmex Scientific Karsten Joensen JJ X Ray Systems Aps Mike Degen Rigaku IT Milos Steinhart Macromolecular Institute in Prague Steen Hansen University of Copenhagen Life Sciences Department Brian Pauw Arhus University Chemistry Department SAXSGUI User Manual v 2 05 02 2 2 0 Getting Started 2 1 Installing SAXSGUI when you have a MATLAB license SAXSGUI requires MATLAB version 7 10 0 2010a or later Presently it comprises 3 toolboxes gt saxsgui Containing the MATLAB files for manipula
45. on bar with instruction will appear at the bottom of the panel The instruction varies a little depending on the type of region sometimes it is click and drag to create a region other times 1t click click click etc The way to stop the creation also differs sometimes just lifting you finger from the mouse button sometimes pressing the keyboard When the region has been created the create button turns red and displays delete At this stage you can 1 Decide whether you to actually want to use this region by checking the appropriate check box in the active column If the region is not active it will not be shown on the figure and it will not influence the mask creation 2 Decide whether you want to exclude the exterior of the region by checking the appropriate radio button in the exclude exterior column If you do not check this it is automatically the interior that is excluded 3 Decide to delete the region completely 4 Edit the points of the region one by one by pressing the edit button When done press the yellow apply button In MATLAB 7 it is sometimes required to press once on the image window after pressing the apply button I don t know why 5 Drag the region one by one by pressing the edit button When done press the yellow apply button In MATLAB 7 it is sometimes required to press once on the image window after pressing the apply button I don t know why Please note that
46. quickly apply the same reduction parameters as the previous image This information is lost when MATLAB 1s closed gt Edit Parameters I This Opens up a panel where you can la xi File specify which reductions are relevant This panel itself has a File menu Apply Done Cancel where you can O Sample Transmission 0 105 gt Save the information contained in A Mask Mask File mask051 204 Browse the panel EE from the panel z Empty Holder Transmission Empty Holder Cap_lr_3600s_2920_4000_3 Browse gt Create Mask for opening up the program maskmakergui where you can create a mask for the data gt Construct an artificial flatfield EEE En m EE from low intensity flatfield a a non flatfields Dark Current curren filename Broyyse Readout Noise Readout Noise File PPSO 1008 mr Browse Save and Load Configuration Configuration 1 Configuration 2 Configuration 3 Configuration 4 Configuration 5 One can see that you can choose to apply one or more of the reductions and corrections by activating the buttons on _Load Existing Load ising ene Lopa eing the left after which one should enter Save above as Saveaboveas Save above as Save above as Save above as the appropriate data in the form of numbers or filenames When the apply button is pressed the information in the SAXSGUI window is updated This reduction window can be left open if several data sets are to be analyzed At the bottom o
47. reduced From the screen dump below you can see that it is possible to gt choose how many points bins you want in your 1D spectrum and whether you want the distribution of these bins to be Linear or Logarithmic gt specify whether reduction should be performed pixel by pixel which requires correction data with good statistics or spectra by spectra For more information on the difference see appendix 2 gt specify plots of azimuthally averaged intensity vs momentum transfer or average intensity vs azimuth angle gt indicate exactly which reductions you would like to apply gt specify the the area that you want to average over either by entering values or by pointing and dragging a rectangle in the right hand image gt Choose to press the same as last buttons if all you want to do is repeat the previous averaging ee m El averagex en quen o ol i Data Reduction and Ave raging Specify a region by entering Left Right Bottom and Top values or drag your pointer in the image CUsersKarsten DocumentsiOld comiFrom C Lett O806 Data BacheniSDSidata 4gBeh_hr2 mpa Same as last 0 0019166 Linear Color Scale 350 Plot azimuthal average intensity vs momentum transfer X axis Binning Linear Logarithmic Number of Points 200 Top of Color Scale 300 Plot average intensity vs azimuth Same as last 4 A 250 Reductions and Corrections 200 Reduction Type Spectra by Spectra Pixebby
48. rks well for SSS uncomplicated reductions but not so well if the Vae fhe aaved time i UE Gand mam Peer transmissions or background files change Tip Add up to 5 formulas to calculate special values for the reduced file for example something like integrated area danesa psc ac iis ce D Saree 1D figures ge Is Deacrpire Tag les j Maskmaker window is spawned through the Edit Reductions File Menu and is used to create a mask for the reduction of images Pixels inside or outside various geometrical figures can be selected for exclusion See Appendix 4 for examples of how to use the maskmaker tool Tip Be sure to save the RONI Region of Non Interest so that it can be used later for easy maskmaking 1000 Region of Non jInterests 900 Exclude Exterior TYPE of RONI Number Active e Circle m 7 Polygon X 800 700 Fes ow il 600 Rectangle Rectangle i 500 N Rectange v Q og 400 Q Rectange v Rectangle i 300 Rectangle ow Q 200 Rectangle v 100 g i 8 j i 100 200 300 400 500 600 700 800 900 1000 Flatfield maker window is also spawned nm through the Edit Reduction window It is used File for constructing pseudo flatfields based on real low intensity flatfields and high intensity non flatfields This tool was created as an alternative CER ME cerns to the often
49. rn Martes ot Pirta 1 Adut ard Comectons Reduction Type T Speret pta T Pehia SAXSGUI User Manual v 2 05 02 29 iam Special Double Background Subtraction in Auto processing mode By request from solution scatterers in Prague we have made a double background subtraction available in the Auto processing mode This 1s intended for case in which you have a capillary filled solvent and sample and another capillary filled with solvent and therefore a different sample thickness In this case one needs to separate out the effect of the different thicknesses and needs additional parameters Here is an info file that would do just that SamplePosition 0 1 Sample Description POS1 Username Date 11 8 2006 10 20 PM Trans Factor 1 000000 LiveTime 60 RealTime 60 Background file Intensity file Flatfield file Dark count file Comments sample_thickness 0 1 background_transmission 0 15 solvent_filename C Data Yale Solution 850 mm 000065 mpa solvent_transmission 0 4 solvent_thickness 0 2 PhotoDiode 730 632E 12 C Data Yale Solution 850 mm 000066 mpa And or one could use the variables o solvent filename C 000066 mpa should be included in the info file solvent transfiact 0 23 should be included in the anio file solvent thickness 0 104 should be included in the info file that were commented out in the example above Note This double Background subtraction is not supported outside
50. rs are mapped to intensity values The color scale controls disappear while you view log intensities Choose this command again to display linear intensity values and restore the color scale controls Grid toggle Display grid lines across images Choose this command again to remove the grid lines gt Zoom toggle Turn zoom control on see below Choose this command again to toggle zoom control off SAXSGUI may turn zoom off automatically after some other commands left click Zoom in at the pointer position right click Zoom to the dragged area double click Zoom out to the full image gt Crosshairs and coordinates toggle Turn on full window crosshairs that follow your pointer Turns on x y coordinate labels that show the current pointer position in terms of each image s axes coordinates Choose this command again to toggle crosshairs and coordinates off gt Projection along Line toggle Brings up a figure and a line in the image The figure shows the pixel values along the line The line may be moved around by using the left button of the mouse to move the edges Known Bug Apparently it appears that right button clicking the mouse kills the functionality gt Color map Choose a different color map to display image intensity values The default map 1s jet Those used to Bruker software may prefer hot while Rigaku software will prefer jet gt Fatpix Open a fatpix window that zooms in to the x y left hand ima
51. s momentum transfer plots For Intensity vs azimuth plots plot content fIvsq ES fIvsq ES Available Available FE vs q2 Available Not Available Note We will gladly add others if it makes sense and 1s requested SAXSGUI User Manual v 2 05 02 19 3 2 3 The Analysis menu This menu item contains a number of possibilities for analyzing the data ranging from a simple statistical analysis to fitting a few generic models to multiparameter fitting of standard and potentially user defined function and finally to a very nice little Inverse Fourier Transform gt QuikStat Allows you to define a region of the curve and the provides you with information on the q range the intensity range and the integrated intensity of the region you selected gt QuikFit This menu provides the opportunity to fit a user designated region of the curve to one of a large i QuikStat EE EET EE 10 QuikFit PeakFit gt Gauss Peak Slope Bckg number of very standard models organized in FullFit PorodFit gt Gauss Peak Spline Bckg main themes The fitting routine does not allow Bayesian FT GuinierFit Lorentz Peak Slope Bckg 10 FractalFi orentz Peak Spline Bc one to enter starting parameters but attempts to ee ee Es PearsonVII Pealc Slope Bckg calculate the starting parameters based on user PearsonVi Peak Spline Bekg 10 Double PearsonVII Peak Slope Bckg clicks on the graphs The optimization scheme 1s a Downhil
52. t be in order later perhaps 9 One is then asked if the result is acceptable and if so then asked to find a filename to save it in ES ppnpinabeaj flathie ac Save Ji Rafie des 0am z Hart Date ken Tags Sant Raters Rosy Meertet 1 Firman LES EE a Maes ao feskion T Ansu ban dE F Messi sie En Kanon Coeguter LL beter Fit p Resad El a Save pa tyor MAT then 7 mat Em And it is done SAXSGUI User Manual v 2 05 02 39 Appendix 6 Special Considerations for a Pilatus 300K Pilatus detectors from the company Dectris are pixellated solid state detectors with individual photon counting capabilities and thus low backgrounds The basic solid state unit has rouhly 100K pixels and covers a 38 by 97 mm area Larger areas are obtained by juxtaposing the basic units A SAXS image of 10 SDS is seen below for a Pilatus 300K LA Ta i O l fie View Alter Cabbrations Beducten Quik Enter Processing Polar Transteemation mage 00167 1d ts ers 3 apewh 4 50 100 150 200 250 300 350 momentum transfer pixels The solid state nature of the detector and the juxtaposition of the basic units provides some additional complexity to the interative data reduction For example 1 2 3 The solid state nature of the detector makes it susceptible to intensity registration of very strong cosmic radiation
53. time consuming flatfield Davi Curren measurements albeit a clearly inferior alternative See the SAXSGUI Demos for an example of how to use the Flatfieldmaker window Law Iinhenetihy FlatFindd lenge Trane SAXSGUI User Manual v 2 05 02 7 3 1 The SAXSGUI Window Controls menus commands The SAXSGUI Window is the entry point into the SAXSGUI programs and panels The version of SAXSGUI is displayed in the top left window name 3 1 1 The File menu This menu contains commands for reading and writing files as well as for setting central SAXSGUI preference gt gt Open Opens an image file replacing whatever image SAXSGUI is displaying If you want to save changes you have made to the previous image use the Save command before opening a new file Open from SPEC file If you have specified that you are working in a SPEC environment in the SAXSGUI settings m file then this menu will be available It opens allows you to open an image file that is listed in a SPEC log file Otherwise it works as open Combine and Open Prompts you to choose a number of images which will then be combined pixel by pixel and opened If the files contain information on exposure time the final image will contain information on the combined exposure time Name Give the SAXS image a new name The name appears above the image display in the SAXSGUI window The Save command saves this new name with the image Save image as Sav
54. ting saxs data gt BIFT A MATLAB tool for performing Bayesian Inverse Fourier Transform on SAXS data gt maskmaker A MATLAB tool for creating masks to use only regions with good SAXS data And these 2 fitting model repositories gt saxsgui f Id a directory containing 1 d model functions callable by saxsgui gt saxsgui f 2d a directory containing 2 d model functions callable by saxsgui In addition the following contributed toolboxes are distributed with limited support gt sampledb a toolbox for making a small database of saxs data Contributed by Brian Pauw gt mysacalibator A toolbox for performing more detailed centering and calibration Contributed by Milos Steinhart These toolboxes can be placed in the MATLABHOME toolbox directory or anywhere you like They should all be entered into the MATLAB path using the File gt Set Path menus Press the save button in the Set Path panel to ensure correct functioning also in later sessions You should also make sure that the setting in the SAXSGUL settings m file in the saxsgui toolbox are correct For example make sure the variables fitfunction dir 2D are defined as the actual pathnames of the model file repository 2 1 Installing SAXSGUI when you do not have a MATLAB license The majority of this manual assumes you are running SAXSGUI with a MATLAB license However for users that do not want to invest ina MATLAB license it 1s possible to run SAXSGUI o
55. used especially when the data has poor statistics One can even see this effect on the example on the next page For this example it is not a huge difference but it is a discernable difference the Pixel by Pixel data is more noisy Note One important case where Spectra by Spectra should be considered is if the flatfield image does not have significant statistics In this case the deviation of intensity distribution deviates from a gausssian distribution and thus makes a significant difference between the two approaches The advantages and disadvantages are summed up below Pixel By Pixel gt Can obtain 2D images Not so robust since pixels gt Can create good pictures for with 0 counts create trouble Caution when using noisy data Fails when using flatfield with poor statistics many zeroes for example Spectra By Spectra Robust Cannot obtain 2D images Work well with typical SAXS data noisy count rate limited SAXSGUI User Manual v 2 05 02 25 Pixel by Pixel Reduction Figure 3 masked Spectra by Spectra Reduction PowderSampled_posd_100s_mir i a SAXSGUI User Manual v 2 05 02 26 Appendix 3 Auto Processing on the Molmet Rigaku SAXS system Auto processing on the Molmet Rigaku SAXS system in implemented through the 2 key files that can be prepared either by the user and or by the LabView SAXS program The first file is the info file generated by LabView SAXS control program e
56. very time an image is saved by the LabView program An example is seen below SamplePosition 5 SamplePositionMM Sample Description Username SANSE Date 5 8 2008 4 40 PM Trans Factor 1 000000 LiveTime 300 RealTime 300 Background file Intensity file Flatfield file Dark count file Comments PhotoDiode 246 566E 12 6 00020 690 252 SAMPLE IN CAPILLARY Ones sees that there is a lot of space for putting in information that is pertinent to the sample If one constructs an appropriate script the generated info file could look like this SamplePosition 0 SamplePositionMM Sample Description Username SANSE Date 11 8 2008 10 20 PM Trans Factor 0 302 Ds O24 OT 329 9 POS1 I e LiveTime 60 RealTime 60 Background file C Data Yale Solution 850 mm 000066 mpa Intensity file Flatfield file Dark count file Comments PhotoDiode 730 632E 12 Although this is better the trained eye would see that there is presently no room for sample thicknesses background file transmissions and other parameters that are specific to the sample being measured so to circumvent this present limitation in the info file we use the Comments spot SamplePosition 0 1 SamplePositionMM 89 524 69 959 Sample Description POS1 Username Date 11 8 2006 10 20 PM Trans Factor 0 245000 LiveTime 60 RealTime 60 Background file C Data 000066 mpa Intensity file Flatfield file

SAXSGUI User Manual v.2.05.02

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