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TOPO Installation Guide and User`s Manual - Reflective X

1. PROCEDURE PROF2SLOPE is used to compute the slope values HEIGHT_DIST is used to compute the slope histogram function MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 4 4 14 PLOT_SLOPE NAME PLOT_SLOPE PURPOSE Procedure to plot a slope function CATEGORY eflective rayOptics 62 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 Topographic analysis CALLING SEQUENCE PLOT_SLOPE X SLOPE INPUTS X 1D array of lengths in units corresponding to the value of TOPO XUNITS_PTR SLOPE 1D array of slope values in degrees KEYWORD PARAMETERS OVERPLOT Set for overplot NOLABEL Set to inhibit labeling the SIGMA and L values LABEL_ POSITION Integer specifying label position as per PLOT_TEXT Plus most IDL PLOT graphics keywords RESTRICTIONS The units for X must correspond to the value of the relevant tag of the common block variable TOPO That is set TOPO XUNITS_PTR to 0 for X in angstroms 1 for nm 2 for microns and 3 for mm The precision of the rms slope parameter that is labeled on the plot is determined by the value of the variable TOPO SPRECISION For example if TOPO SPRECISION 3 then three places to the right of the decimal will be displayed MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 4 4 15 PROF2AUTOCOV NAME PROF 2AUTOCOV PURPOSE Function to compute the autocovariance function
2. N TOPO_psd is essentially a wrapper for the PLOT_PSD routine described in 4 4 12 IDL Programmers should consult 4 3 2 for more information on the TOPO_psd routine eflective rayOptics 21 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs S iE TOPO PSD Analysis HS py gt File Preferences Units Precision 10000 0 1060 0 160 0 opectral er ow 1 OD Spatial Frequency f 1 A Options available from the TOPO_psd menu bar are similar to those described above for the TOPO_prof routine As explained in 84 3 2 the TWOD keyword to the TOPO_psd procedure can be set to indicate that the F and S values correspond to a 1D slice of a 2D PSD function or a radially averaged PSD function Note When TWOD is set S must be defined in units of Ai If the TWOD keyword has been set or if you start TOPO_psd by clicking the button labeled TOPO_psd 1D power spectral density analysis TWOD on TOPO Launcher then the PSD fit type displayed by default is the Q v n PSD model explained in Stearns et al 3 Other fit options for 2D PSD data available from the Preferences gt Axis Fitting Style menu option are the o amp H PSD model 4 as well as a power law 2 eflective rayOptics 22 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs Note The best fit parameters derived using the Q v n or the o amp H PS
3. Z Db unto Ready Reflective rayOptics 8 7 October 2013 TOPO Version 2 2 TOPO Installation Guide 7 The TOPO splash screen will appear Click OK to start TOPO Launcher and load the TOPO library of IDL routines From TOPO Launcher you can run the GUI programs TOPO Multiplot TOPO_ prof TOPO_psd and TOPO _surf File Help TOPO Muttiplot TOPO_prof 1D profile analysis TOPO_psd 1D power spectral density analysis TOPO_psd 1D power spectral density analysis TWOD TOPO_surf 2D surface analysis 8 You re up and running Now please read the rest of TOPO pdf so that you get the most out of TOPO Also check out the IMD amp TOPO Google group https groups google com forum forum imd_ topo for discussion and announcements of future releases Reflective rayOptics 9 7 October 2013 TOPO Version 2 2 TOPO Installation Guide 1 3 Installing TOPO as an XOP extension If you will NOT use TOPO as an XOP extension then you can skip this section and proceed to 1 4 Once you have XOP installed and running on your computer follow these steps to install and run TOPO 1 5 Download the TOPO installation file topo_xxx tar gz from http www rxollc com idl xxx version number for example topo_2 2 tar gz Unpack the topo_xxx tar gz file containing the topo installation directory e For Windows use a program like Winzip to open topo_xxx tar gz e For Linux Mac OS X Solaris use the gun
4. 7 October 2013 TOPO Version 2 2 TOPO User s Manual 4 TOPO for IDL Programmers CALLING SEQUENCE Result HEIGHT_DIST X Y HEIGHTS INPUTS X 1D array of equally spaced lengths Y 1D array of heights KEYWORD PARAMETERS N_HTS Integer specifying the number of bins to be used in conjunction with the HISTOGRAM function RANGE 2 element array specifying the min and max height values to consider OUTPUTS Result 1D array of density values See the HISTOGRAM function OPTIONAL OUTPUTS HEIGHTS 1D array of height values the i th element of Result is the density of heights in the i th bin of HEIGHTS PROCEDURE The HISTOGRAM function is used MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 4 4 7 PARS2AUTOCOV NAME PARS2AUTOCOV PURPOSE Function to generate an autocovariance function from an array of parameters describing the function This function is a sort of inverse of the AUTOCOV_FIT routine CATEGORY Topographic analysis CALLING SEQUENCE C PARS2AUTOCOV TAUX TAUY P TYPE TYPE INPUTS TAUX 1D array of lag lengths along X direction TAUY Optional 1D array of lag lengths along Y direction P Array of parameters describing the function The number of elements of P required depends on the value of the TYPE keyword TYPE Keyword specifying the functional form for C 0 for eflective rayOptics 55 7 October 2013 TOPO Version 2 2 TOPO User s Manual 4
5. NewY SUB_TILT X Y MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 4 4 27 SURF2AVE_PSD NAME SURF 2AVE_PSD PURPOSE Procedure to compute the average power spectral density functions along X and Y from surface data CATEGORY Topographic analysis CALLING SEQUENCE SURF2AVE_PSD X Y Z XAVEPSD XAVEPSD YAVEPSD YAVEPSD FX FX FY FY XPSD XPSD YPSD YPSD eflective rayOptics 72 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 INPUTS X 1D array of lengths along X direction Y 1D array of lengths along Y direction Z 2D array of heights OUTPUTS FX 1D array of spatial frequencies along X direction units of 1 X FY 1D array of spatial frequencies along Y direction units of 1 Y TOPO User s Manual 4 TOPO for IDL Programmers in in XAVEPSD 1D array of PSD values average of XPSD along Y direction in units of Z 73 YAVEPSD 1D array of PSD values average of YPSD along X direction in units of Z 73 XPSD 2D array of PSD values computed along X direction in units of Z 73 YPSD 2D array of PSD values computed along Y direction in units of Z 73 KEYWORD PARAMETERS POSITIVE_ONLY Set to compute the autocovariance function for positive lag lengths only RANGE 2 element array specifying the min and max spatial frequencies to be considered Default is from 1 length to 1 2 interval
6. Title M Subtitle F X Min 0 00000000 Max 0 00000000 M Exact TC Log I Grid Title F Y Min 0 00000000 Max 0 00000000 TC Exact flog TC Grid Title E Z Min 0 00000000 Max 0 00000000 M Eat I Log Tile E l Done Refresh Rename Add Piot Files eflective rayOptics 30 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs The drop list labeled Plot Type circled in the previous figure is used to select the type of plot displayed with a variety of other options For example the next figure shows the Radially Averaged PSD computed from this same data File Screen Color Units Precision Plot 1 a Plot Type PSD Radially Average y None Height 2D Contour Legend Height 3D Surface Condensed Colo y Height Histogram PSD 2D Contour PSD RE None cp 3D Surface P PSD X Averaged i Title PSD Y Averaged Subtitle F X min 0 00000000 Max 0 00000000 M Exact log W Gid Ttle Y Min 0 00000000 Max 0 00000000 M Eat M Log W Gid gei E Done Refresh Renam Add Plot D Fies ES There are a variety of controls to adjust the plot appearance e g titles axes ranges grid lines etc and additional controls specific to the type of plot being displayed The button labeled Add Plot circled in red a
7. 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 TOPO User s Manual 4 TOPO for IDL Programmers Function to fit a 1D array of power spectral density function values with a power law CATEGORY Topographic analysis CALLING SEQUENCE Result PSD_FIT F S PARS INPUTS F 1D array of spatial frequencies S 1D array of power spectral density values OUTPUTS Result Fit function PARS 1 D array of fit parameters PARS 0 K_n PARS 1 N KEYWORD PARAMETERS RANGE 2 element array of min and max spatial frequencies to be used for fitting Default is to use the entire range of data FFIT Array of F values corresponding to the range used for fitting TWOD If TWOD is set then the 1D array of PSD values is consider to represent a slice or radial average of a 2D PSD function PROCEDURE A 1D PSD function is fit to the function S K_n ABS F N A 2D PSD function is fit to the function S Gamma N 1 2 2 Gamma 1 2 Gamma N 2 K_n F N 1 MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 May 1998 Added RANGE FFIT and TWOD keywords If a 2 sided PSD is provided then fit function returned is now only 1 sided i e defined only for positive frequencies 4 4 19 PSD_FIT_OMEGA_NU_N NAME PSD_OMEGA_NU_N_FIT PURPOSE Function to fit a power spectral density function with a function of the form PSD 2 pi F Omega 1 exp 2 nu 2 pi F n z 2 nu
8. TOPO for IDL Programmers Gaussian 1 for exponential 2 for Gaussiant texponential OUTPUTS C 1D or 2D array of autocovariance values PROCEDURE TYPE 0 Gaussian C P 0 2 EXP TAU P 1 2 P 2 TYPE 1 Exponential C P 0 2 EXP ABS TAU P 1 P 2 TYPE 2 Gaussian Exponential C P 0 2 EXP TAU P 1 72 P 2 2 EXP ABS TAU P 3 P 4 MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 4 4 8 PARS2PSD NAME PARS2PSD PURPOSE Function to generate a power law power spectral density function from an array of parameters describing the function This function is a sort of inverse of the PSD_FIT routine CATEGORY Topographic analysis CALLING SEQUENCE S PARS2PSD FX FY P INPUTS FX 1D output array of spatial frequencies along X direction FY 1D output array of spatial frequencies along Y direction P 2 element array of parameters describing the power law function P 0 En P 1 n OUTPUTS S 1D or 2D array of power spectral density values PROCEDURE For a 1D PSD function S P 0 ABS F P 1 For a 2D PSD function eflective rayOptics 56 7 October 2013 TOPO Version 2 2 S GAMMA P 1 1 2 2 GAMMA 5 GAMMA P 1 2 P 0 ABS F P 1 1 MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 4 4 9 PLOT_AUTOCOV NAME PLOT_AUTOCOV PURPOSE Procedure to plot and optionally fit the aut
9. menu option described above The menu options Analysis gt Radially Averaged PSD and Analysis X and Y Averaged PSD can be used to compute from the 2D surface data the radially averaged PSD using the SURF2PSD 4 4 28 and PSD2RAVEPSD 4 4 23 routines and the X and Y averaged PSDs i e the average of all the 1D PSDs computed from each row or column of the image respectively using the SURF2AVE_PSD routine 4 4 27 which are then displayed in new TOPO_psd windows these quantities can then be exported to plain text files from TOPO_psd eflective rayOptics 26 7 October 2013 TOPO Version 2 2 3 4 TOPO Multiplot TOPO User s Manual 3 TOPO Launcher Programs The TOPO Multiplot routine is used to analyze and visualize one or more 2D surface data files TOPO Multiplot can be run directly from TOPO Launcher or it can be run from the IDL command line using the syntax IDL gt topomultiplot When TOPO Multiplot is first started it looks like this El Plot Type Height 2D Contour e Plot Array E x 1 Includef FileName Date XY TI RP Color Table lLevels all de gt MV Color Bar Title X Min 0 00000000 Max 0 00000000 Log Y Min 0 00000000 Max 0 00000000 Z Min 0 00000000 Max 0 00000000 Log Log r Grid Grid Subtitle File Screen Color Units Precision Plot 1 Done Refresh Re
10. rayOptics 10 7 October 2013 TOPO Version 2 2 TOPO Installation Guide 6 The TOPO splash screen will appear Click OK to start TOPO Launcher From TOPO Launcher you can run the GUI programs TOPO Multiplot TOPO_prof TOPO_psd and TOPO_ surf File Help TOPO_prof 1D profile analysis TOPO_psd 1D power spectral density analysis TOPO _psd 1D power spectral density analysis TWOD TOPO_surf 2D surface analysis 7 You re up and running Now please read the rest of TOPO pdf so that you get the most out of TOPO Also check out the IMD amp TOPO Google group https groups google com forum forum imd_ topo for discussion and announcements of future releases Reflective rayOptics 11 7 October 2013 TOPO Version 2 2 TOPO Installation Guide 1 4 Customizing the TOPO installation topo_cfg pro 1 4 1 Non standard installation location If you will use TOPO with a licensed copy of IDL and you choose not to install the TOPO installation directory in the default location Le the user_contrib directory in the main IDL directory as described in 1 2 then you must edit the TOPO configuration file topo_cfg pro which is located in the topo installation directory you have selected specifically using any plain text editor change the value of the topo_home variable defined in this file so that it refers to the actual location where you ve installed the topo directory on your computer EXAMPLE You are using a lin
11. 2 4 2 2 RD MICROMAP PAP donee 42 4 2 3 RD NANOSCOPE wz caccecpcdesaseeecccvctevsateieseetesougnascusescea sens cesote ote ccdsegedusnsesbeceustesevente geacteasgoest 42 4 2 4 RD WYKO TOP OSD iii tect eh Ae ne E E 43 4 2 5 RD ZY GO NEW VIEW EE 44 4 3 TOPO Launcher GUI ROUTINES ccccccccesceceessscececssscececssesececssececsseseceessseceesesecsesesaeeeessesess 44 4 3 1 TOPO aaa 44 4 3 2 TOPO OSC EE 46 4 3 3 TOPO SUMP SE 47 4 3 4 TOPO OT e 48 4 4 Computational and Graphics Routines ooooccccnccanonooaoncnnnnnnanononnnnnnnnnnnnnnno nn nnnnncnnnnnnnrnnnnnnncanannnns 49 4 4 1 NEIE ST 49 4 4 2 ANLZ PRO Ritos oia 50 4 4 3 AUTOCON HME 52 4 4 4 NR ele UE 53 4 4 5 PUT OCOV2ZPS D sia 54 4 4 6 HEIGHT DIST EE 54 4 4 7 PARS2AUTOCON eeneg ti ada 55 4 4 8 PARS2 KEE 56 4 4 9 PLOT AUTOCO TE 57 BOAO PLOT H Di Teis 58 AAJ PLOT RRE ir ti di ege 59 A A O eegen 60 44 13 PLOTS DIST WEE 61 OAs PILOT SSO EE 62 24 15 PROF2AUTOCON eegener Ee ENEE nadaa aid danes idas 63 44 16 PROF2P Disc a dt a eee 64 44 17 PROF2SLOPE cuidada ads 65 A Re El e 65 A A 19 A NA 66 EIERE A kteri taret aa nennen nnen rennrr rens 67 4421 PSD2AUTOCOV EE 68 eflective rayOptics 4 7 October 2013 TOPO Version 2 2 BADD A RN 69 44 23 PSDIRAVEP SD iii Ai ia 69 4 4 24 PSDPARS_ANGLE2SIGMA L A 70 4 4 25 PSDPARS2SIGMA Lagere eeeg ee seed eege EEN et Eege EE 71 44 26 SUB TILT E 72 44 27 SURF2ZAVE BEID geseet va sadacevaacaece satdant
12. 3 gt microns and 4 gt mm KEYWORD PARAMETERS TO_ANGSTROMS Set to convert an input Y from the units specified by TOPO YUNITS_PTR to angstroms COMMON BLOCKS COMMON TOPO MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 eflective rayOptics 76 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 5 Performance and Troubleshooting This version of TOPO was developed almost entirely on a linux platform CentOS using IDL 6 3 since it was released in 2007 and previous versions of IDL before that Some rudimentary testing was performed on Windows 7 while this document was being written and the example files were being created you may recognize the screen captures as coming from Win7 Windows 7 testing was performed using either IDL 6 3 or XOP 2 3 which in turn uses IDL 7 The linux version was also tested briefly prior to release using IDL 8 2 3 and on Mac OS X minimal testing using XOP 2 3 was performed as well If you find any performance issues on these or any other platforms please don t hesitate to let me know 5 1 Frequently Asked Questions 5 1 1 Q I can t get TOPO to work start A Check that you ve installed TOPO exactly as per the instructions See 1 5 5 1 2 Q Can I get a copy of the TOPO source code A No Sorry 5 1 3 Q Will can you include feature X in a future release of TOPO A Maybe Tell me about it 5 1 4 Q Will TOPO work with t
13. A files e blue solid lines and for the two Sample B files i e pink solid lines These settings will be used in any Histogram or 1D PSD graphics we choose to display Reflective rayOptics 35 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs One plot tab on the main TOPO Multiplot window in this example tmp file has been configured to display all four AFM images in a 2x2 grid a second plot tab displays the radially averaged PSDs computed from each image Here s how those two tabs appear after setting the background to white using the Screen Color gt Black on White menu option 5 TOPO Multiplot C File Screen Color Units Precision Images PSD Sample A Position Y em Position Y um 1 0 i 2 0 6 A Position X tem Position X gm Sen dng Sen lu Sample B Sample B Height Z A 3 A gt gt g E 2 5 E 2 p kal ES a a CG 1 0 ge 2 0 DZ 4 6 A Position X em Position X wm e RM nX Jeg Q Piot Type Height 2D Contour e Plot Aray D x 2 be FileName Date M XY I pp Color Table heves j a gt JW Color Bar Tlf ttle K Min 0 00000000 Max 0 00000000 TExra M Log I Grid Y min 0 00000000 Max 0 00000000 I Exact I Log I Grid Z Min 10 000000 Max 10 000000 ss Bact I Log Reflective rayOptics 36 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs IE TOPO Multiplot File Screen Co
14. FIT_TYPE is specified SFIT Output fit dependent variable FFIT Output fit independent variable FIT_PARS Fit parameters See PSD_FIT FIT_COLOR IDL graphics keyword for fit function FIT_THICK IDL graphics keyword for fit function FIT_LINESTYLE IDL graphics keyword for fit function NOLABEL Set to inhibit labeling the SIGMA L and fit parameters values LABEL_ POSITION Integer specifying label position as per PLOT_TEXT Plus most IDL PLOT graphics keywords RESTRICTIONS MODIF The units for F and S must correspond to the values of the relevant tags of the common block variable TOPO That is set TOPO XUNITS_PTR to 0 for F in angstroms 1 for nm 2 for microns and 3 for mm Similarly set TOPO YUNITS_PTR to 0 for S in angstroms 3 1 for nm 3 2 for microns 3 and 3 for mm 3 The precision of the fit parameters that are labeled on the plot is determined by the values of the variables TOPO XPRECISION for length related parameters e g correlation length and TOPO YPRECISION for height related parameters e g rms roughness For example if TOPO XPRECISION 3 then three places to the right of the decimal will be displayed CATION HISTORY David L Windt Bell Laboratories May 1997 May 1998 Added FIT_TYPE 1 2 and REGION and Z_VALUE keywords F and S are now correctly converted according the values of TOPO XUNITS_PTR and TOPO YUNITS_PTR 4 4 13 PLOT_S_DIST NAME PURP
15. TOPOMULTIPLOT PURPOSE A widget application for analysis of one or more 2D surface data files CATEGORY Topographic analysis CALLING SEQUENCE TOPOMULTIPLOT KEYWORDS GROUP Widget GROUP_LEADER keyword to XMANAGER WID The widget id of the TOPOMULTIPLOT base You can use the widget id to destroy the widget programmatically FILE The name of a TOPO Multiplot tmp file to open at startup COMMON BLOCKS COMMON TOPO COMMON PLOT_PRINT PROCEDURE See 3 4 eflective rayOptics 48 7 October 2013 TOPO Version 2 2 4 4 Computational and Graphics Routines 4 4 1 ANGLE2WAVES NAME ANGLE2WAVES PURPOSE Procedure to compute and optionally plot the spatial wavelengths corresponding to scattering for incidence angle ALPHA wavelength LAMBDA into scattering angles ALPHA DELTA 0 to ALPHA DELTA 1 CATEGORY Topographic analysis CALLING SEQUENCE ANGLE2WAVES ALPHA LAMBDA DELTA WAVES WAVES INPUTS ALPHA A scalar or 1D array of incidence angles LAMBDA Scalar specifying the incidence wavelength DELTA 2 element array specifying the min and max scattering angles to consider KEYWORD PARAMETERS WAVES Output array of spatial wavelengths having dimensions 2 N_ELEMENTS ALPHA Units are the same as for LAMBDA The following keywords only have an effect when ALPHA is an array NOPLOT Set to inhibit plotting the results All IDL PLOT graphics keywords PROCEDURE WAVES
16. X Y 2Z KEYWORD PARAMETERS FILE name of Nanoscope III data file TILT_SUB set to subtract tilt SPHERE_SUB set to subtract a 2nd order polynomial background HIST_EQUAL set to perform histogram equalization of image SWAP_ENDIAN set to use the SWAP_ENDIAN function to convert the data file from big endian to little endian or visa versa Useful for reading on a eflective rayOptics 42 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 Windows platform data files originally stored on Unix or Mac platforms or visa versa OUTPUTS X Vector of x position values in angstroms Y Vector of y position values in angstroms Z Array of height values in angstroms MODIFICATION HISTORY David L Windt Bell Labs 1992 aka RD_DIGITAL_AFM 4 2 4 RD_WYKO_TOPO3D NAME RD_WYKO_TOPO3D PURPOSE Read a WYKO TOPO 3D data file CALLING SEQUENCE RD_WYKO_TOPO3D FILE FILE X Y 2 HEADER HEADER KEYWORD PARAMETERS FILE name of WYKO data file OFFSET set OFFSET to skip an additional 512 bytes at the beginning of the data file This additional 512 byte header is introduced by BASIC UX when the file is transferred from an LIF to an HFS disk TILT_SUB set to subtract tilt SPHERE_SUB set to subtract a 2nd order polynomial background HIST_EQUAL set to perform histogram equalization of image SWAP_ENDIAN set to use the SWAP_ENDIAN function to convert the dat
17. constant i e independent of your choice of window September 2000 Corrected a problem wherein the spatial frequencies were computed incorrectly Also non isotropic surfaces are now handled correctly Much thanks to Eric Gullikson LBL EMGullikson lbl gov 4 4 29 TOPO_X_CONVERT NAME TOPO_X_CONVERT PURPOSE Function to convert length variables according to the value of the common block variable TOPO XUNITS_PTR CATEGORY Topographic analysis CALLING SEQUENCE NewX TOPO_X_CONVERT X INPUTS X 1D array of length values in angstroms OUTPUTS Result 1D array of length values in units specified by TOPO XUNITS_PTR i e 1 gt angstroms 2 gt nm 3 gt microns and 4 gt mm KEYWORD PARAMETERS TO_ANGSTROMS Set to convert an input X from the units specified by TOPO XUNITS_PTR to angstroms COMMON BLOCKS COMMON TOPO MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 4 4 30 TOPO_Y_CONVERT NAME TOPO_Y_CONVERT PURPOSE Function to convert height variables according to the value of the common block variable TOPO YUNITS_PTR eflective rayOptics 75 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 CATEGORY Topographic analysis CALLING SEQUENCE NewY TOPO_Y_CONVERT Y INPUTS Y 1D array of height values in angstroms OUTPUTS Result 1D array of height values in units specified by TOPO YUNITS_PTR i e 1 gt angstroms 2 gt nm
18. from the profile data CATEGORY Topographic analysis CALLING SEQUENCE C PROF2AUTOCOV X Y TAU TAU INPUTS X 1D array of equally spaced lengths Y 1D array of heights OUTPUTS eflective rayOptics 63 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 TAU 1D array of lag lengths in units of X C 1D array of autocovariance values in units of Y 2 KEYWORD PARAMETERS POSITIVE_ONLY Set to compute the autocovariance function for positive lag lengths only RESTRICTIONS The X values must be equally spaced MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 4 4 16 PROF2PSD NAME PROF2PSD PURPOSE Function to compute the power spectral density function from the profile data CATEGORY Topographic analysis CALLING SEQUENCE S PROF2PSD X Y F F INPUTS X 1D array of equally spaced lengths Y 1D array of heights OUTPUTS F 1D array of spatial frequencies in units of 1 X S 1D array of PSD values in units of Y 3 KEYWORD PARAMETERS POSITIVE_ONLY Set to compute the psd function for positive frequencies only RANGE 2 element array specifying the min and max spatial frequencies to be considered Default is from 1 length to 1 2 interval i e the Nyquist frequency where length is the length of the scan and interval is the spacing between points ZERO_PAD Set this to an integer specifying the numb
19. i e the Nyquist frequency where length is the length of the scan and interval is the spacing between points ZERO_PAD Set this to an integer specifying the number of zero height points to add on either side of the profile data HANNING Set this to use a Hanning window function KAISER Set this to use a Kaiser Bessel window function PROCEDURE This function computes the 1D PSD functions along every line in the X and Y directions of the image array and then computes the averages in X and Y of these 1D PSD functions Note that SUB_TILT is used on each line prior to computing the PSD MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 windt astro columbia edu September 2000 Corrected a problem that caused SURF2AVE_PSD to fail if X and or Y contained an odd number of points 4 4 28 SURF2PSD NAME SURF 2PSD eflective rayOptics 73 7 October 2013 TOPO Version 2 2 PURPOSE Function to compute the 2D power spectral density function from surface data CATEGORY Topographic analysis CALLING SEQUENCE S SURF2PSD X Y Z FX FX FY FY INPUTS X 1D array of lengths along X direction Y 1D array of lengths along Y direction Z 2D array of heights OUTPUTS Result 2D PSD function in units of Z 4 FX 1D array of spatial frequencies along X direction units of 1 X FY 1D array of spatial frequencies along Y direction units of 1 Y KEYWORD P
20. idl xxx version number for example topo_2 2 tar gz 3 Unpack the topo_xxx tar gz file containing the topo installation directory e For Windows use a program like Winzip to open topo_xxx tar gz e For Linux Mac OS X Solaris use the gunzip command Sgunzip topo_xxx tar gz followed by the tar command Star xvf topo_xxx tar 4 Move the TOPO installation directory to the user_cont rib directory created in step 1 i e to idl user_contrib topo 5 Start IDL and add the new user _contrib directory just created in step 1 to your IDL search path Consult the IDL documentation for help configuring the IDL_PATH environment variable If setting IDL_PATH manually be sure to include a sign so that the subdirectories under user_contrib will be included e g IDL_PATH usr local rsi idl user_contrib If you re using IDL s Preferences GUI to set the search path be sure to check the search subdirectories box eflective rayOptics 7 7 October 2013 TOPO Version 2 2 TOPO Installation Guide Preferences General Layout Graphics Editor Startup Fonts Path Search path iv Q RSINIDLES user contrib 6 After your IDL search path has been redefined in step 5 type run topo at the IDL prompt to start TOPO IDL Version 6 3 Microsoft Windows W in32 x86 m32 c 2006 Research Systems Inc Installation number 15938 Licensed for personal use by David Windt only Al other use is strictly prohibited
21. in A 3 KEYWORD PARAMETERS TWOD Set to indicate that the F and S values correspond to a 1D slice of a 2D PSD function or a radially averaged PSD function GROUP Widget GROUP_LEADER keyword to XMANAGER COMMON BLOCKS COMMON TOPO COMMON PLOT_PRINT PROCEDURE Although F and S must be in angstroms the units for displayed variables are determined by the values of the relevant tags of the common block variable TOPO That is set TOPO XUNITS_PTR to 0 for angstroms 1 for nm 2 for microns and 3 for mm Same goes for TOPO YUNITS_PTR The precision of the fit parameters that are labeled on the plots is determined by the values of the variables TOPO XPRECISION for length related parameters e g correlation length TOPO YPRECISION for height related parameters e g rms roughness and TOPO SPRECISION for slope related parameters e g rms slope For example if TOPO XPRECISION 3 then three places to the right of the decimal will be displayed The TOPO UNITS_PTR and TOPO PRECISION variables can either be set explicitly before executing this procedure or they can be set transparently to the user be selecting the appropriate menu items once the procedure is running If no data are passed the user is prompted to enter the IDL command string used to read in new data This command string must explicitly define F and S in angstroms For example if your data is in the form of a plain text ASCII file consisting of t
22. in same units as TAU PROCEDURE SIGMA SQRT C L 2 SIGMA 4 Integral C 2 MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 eflective rayOptics 53 7 October 2013 TOPO Version 2 2 44 5 AUTOCOV2PSD NAME AUTOCOV2PSD PURPOSE Function to compute the power spectral density function SIE from the autocovariance function C TAU CATEGORY Topographic analysis CALLING SEQUENCE S AUTOCOV2PSD TAUX TAUY C INPUTS TAUX 1D array of lag lengths along X direction TAUY Optional 1D array of lag lengths along Y direction C 1D or 2D array of autocovariance values OUTPUTS S 1D or 2D array of power spectral density values KEYWORD PARAMETERS FX 1D output array of spatial frequencies along X direction FY 1D output array of spatial frequencies along Y direction POSITIVE_ONLY Set to only compute S F for positive spatial frequencies HANNING Set to use a Hanning window function RANGE 2 element array specifying the min and max spatial frequency values to be considered MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 4 4 6 HEIGHT_DIST NAME HEIGHT _DIST PURPOSE Function to compute the height histogram from X Y profile data The function can also be used to compute the slope histogram in conjunction with the PROF2SLOPE function CATEGORY Topographic analysis eflective rayOptics 54 TOPO User s Manual 4 TOPO for IDL Programmers
23. nm 1D array of spatial frequencies along Y direction in TOPO User s Manual 4 TOPO for IDL Programmers units corresponding to the val lue of TOPO XUNITS_PTR For example if TOPO XUNITS_PTR 1 then FY 1 nm 1D array of power spectral density values in units corresponding to the value of TOPO YUNITS_PTR For example TOPO YUNITS_PTR 1 then S nm 3 E vs at KEYWORD PARAMETERS OVERPLOT Set for overplot SIGMA Rms roughness computed from S using PSD2PARS CORR_LENGTH Correlation length computed from S using PSD2PARS FIT_TYPE Set to 1 for no fit 0 for power law fit 1 for sigma xi h fit and 2 for omega nu n fit If FIT_TYPE 2 then Z VALUE must be provided Note that then TWOD will be set to then if FIT_TYPE is set to 0 zero as well if FIT_TYPE is set to 1 or 2 TWOD will be set to 1 Z_VALUE Film thickness parameter needed for omega nu n PSD model fit Units for Z_VALUE are given by the value of TOPO XUNITS_PTR eflective rayOptics 60 7 October 2013 TOPO Version 2 2 TOPO User s Manual 4 TOPO for IDL Programmers RANGE 2 element array of frequency values defining the region of interest for fitting REGION Set to interactively select a region of interest for fitting using GET_ROI TWOD Set to indicate that the 1D PSD being plotted is actually a slice from a 2D PSD function so that the units are labeled properly This keyword may be overwritten if
24. of TOPO YUNITS_PTR KEYWORD PARAMETERS OVERPLOT Set for overplot NOLABEL Set to inhibit labeling the SIGMA and L values LABEL_ POSITION Integer specifying label position as per PLOT_TEXT Plus most IDL PLOT graphics keywords RESTRICTIONS The units for X and Y must correspond to the values of the relevant tags of the common block variable TOPO That is set eflective rayOptics 59 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 TOPO XUNITS_PTR to 0 for X in angstroms for nm 2 for microns and 3 for mm Similarly set TOPO YUNITS_PTR to 0 for Y in angstroms 1 for nm 2 for microns and 3 for mm The precision of the parameters that are labeled on the plot is determined by the values of the variables TOPO XPRECISION for length related parameters e g correlation length and TOPO YPRECISION for height related parameters e g rms roughness For example if TOPO XPRECISION 3 then three places to the right of the decimal will be displayed MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 4 4 12 PLOT_PSD NAME PLOT_PSD PURPOSE Procedure to plot and optionally fit the power spectral density function CATEGORY Topographic analysis CALLING SEQUENCE PLOT_PSD FX FY S INPUTS FX 1D array of spatial frequencies along X direction in units corresponding to the value of TOPO XUNITS_PTR For example if TOPO XUNITS_PTR 1 then FX 1
25. this kou these computed functions can also be exported as plain text files by clicking the corresponding Export buttons that look like this CH The row of controls with the Plot Style label are used to adjust the display of any 1D functions e g Height Histograms and PSDs that you may choose to plot in TOPO Multiplot as well explain below The next row shows the P V and RMS roughness values computed from the surface data included any limits on Z you may have specified the check boxes can be used to include these values in TOPO Multiplot Reflective rayOptics 29 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs graphics as we ll also explain below The last row includes four text boxes where you can enter X Y or R Phi position values these quantities are meant to refer to the measurement location on the sample surface and are only used for plot labels and legends as well explain After loading a surface data file following the procedure just described return to the main TOPO Multiplot window and click the Refresh button By default a 2D contour of the image will be displayed as in the next figure where we ve also set Length units to um File Screen Color Units Precision Plot 1 A z A Height Z Plot Aray DI x i IncludeS FileName Date M XY I RPhi Color Table levels 7 0 gt MV Color Bar i
26. 05 9 34 AM 136 KB 520 KB 532 KB 520 KB 552 KB DAT File DAT File DAT File DAT File DAT File Ly profile_data_example bd 9 2 2013 7 38 PM 18 KB TXT File L PSD_r_example bdt E PSD_x_example bd _ topomultiplot_example_1_measurement hr topomultiplot_example_1_measurement_ 8 topomultiplot_example_1_measurement_ a topomultiplot_example_1_measurement_ 8 topomultiplot_example 1_measurement_ FE tonomultinlot examnle 1 measurement 9 2 2013 7 33 PM 9 2 2013 7 31 PM 9 2 2013 10 10 PM 2 2013 10 18 PM 2 2013 10 16 PM 2 2013 10 18 PM 2013 10 15 PM 7 2013 10 18 PM 2 gt 9 KB 9 KB 1 757 KB 4 KB 8 KB 45 KB 573 KB 13 KR TXT File TXT File TMP File Adobe Acrobat D PS File Adobe Acrobat D PS File Adohe Acrohat D File name profile_data_example bd After opening the surface profile data file TOPO_prof displays by default a a plot of Y as a function of X with the peak to valley P V and rms roughness o values computed from the profile data indicated on the plot b plots of the surface height and surface slope distributions with Gaussian fits and best fit widths displayed c a plot and fit of the autocovariance function computed from the X Y profile data and d a plot and fit of the power spectral density PSD function computed from the X Y profile data eflective rayOptics 17 7 October 2013 TOPO Version 2 2
27. 2 pi F n eflective rayOptics 66 7 October 2013 TOPO Version 2 2 TOPO User s Manual 4 TOPO for IDL Programmers Note that this form refers to a 2D PSD function thus it only makes sense to use this program to fit a 1D array of radially averaged PSD values This form of the PSD comes from the stochastic model of thin film growth and erosion developed by D Stearns Appl Phys Lett 62 1745 1747 1993 CATEGORY Topographic analysis CALLING SEQUENCE Result PSD_OMEGA_NU_N_FIT F S Z PARS INPUTS F 1D array of spatial frequencies S 1D array of power spectral density values Z z parameter film thickness OUTPUTS Result Fit function PARS 1 D array of fit parameters Omega nu n KEYWORD PARAMETERS RANGE 2 element array of min and max spatial frequencies to be used for fitting Default is to use the entire range of data FFIT Array of F values corresponding to the range used for fitting COMMON BLOCKS COMMON PSD_OMEGA_NU_N Z RESTRICTIONS F and S must use the same length units MODIFICATION HISTORY David L Windt Bell Laboratories May 1998 4 4 20 PSD_FIT_SIGMA_XI_H NAME PSD_SIGMA XI_H FIT PURPOSE Function to fit a power spectral density function with a function of the form PSD 2 pi F 4 pi H sigma 2 xi 2 1 abs 2 pi F 2 xi 2 14H Note that this form refers to a 2D PSD function thus it only makes sense to use this program to fit a 1D array o
28. ARAMETERS in in POSITIVE_ONLY Set to compute the autocovariance function for positive lag lengths only XRANGE 2 element array specifying the min and max spatial frequencies along X direction to be considered Default is from 1 Xlength to 1 2 interval i e the Nyquist frequency Xlength is the length of the scan along X interval is the spacing between points where YRANGE 2 element array specifying the min and max spatial frequencies along Y direction to be considered Default is from 1 Ylength to 1 2 interval i e the Nyquist frequency Ylength is the length of the scan alogn Y interval is the spacing between points where ZERO_PAD Set this to an integer specifying the number of zero height points to add on either side of the profile data HANNING Set this to use a Hanning window function KAISER Set this to use a Kaiser Bessel window function PROCEDURE S XLength YLength ABS FFT Z Window 1 2 Where XLength and YLength are as described above and Window is the value of the optional window function Hanning or Kaiser Bessel MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 eflective rayOptics 74 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 windt astro columbia edu Nov 1998 When using the HANNING or KAISER keywords the window function is now normalized so that the integral of the PSD is
29. BLE Array 10 V 1 NAME STRING Second One V 2 VALUE DOUBLE Array 10 V 2 NAME STRING Another Variable Name MODIFICATION HISTORY David L Windt Bell Labs March 1990 January 1997 DLW Modified to ignore lines beginning with semicolons and to accept data separated by tabs etc Removed the NOTITLE and COMMENT keyword included PICKFILE to prompt for filenames when not specified June 1997 DLW Returned numeric variables are now double precision instead of floating point DLW May 2003 Added V COMMENTS GROUP and CANCEL keywords Replaced call to PICKFILE with call to DIALOG_PICKFILE eflective rayOptics 41 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 4 2 2 RD_MICROMAP NAME RD_MICROMAP PURPOSE Read a Micromap data file CALLING SEQUENCE RD_MICROMAP FILE FILE X Y Z KEYWORD PARAMETERS FILE name of Micromap data file TILT_SUB set to subtract tilt SPHERE_SUB set to subtract a 2nd order polynomial background HIST_EQUAL set to perform histogram equalization of image OUTPUTS X Vector of x position values in angstroms Y Vector of y position values in angstroms Z Array of height values in angstroms MODIFICATION HISTORY David L Windt Bell Laboratories May 1998 4 2 3 RD_NANOSCOPE NAME RD_NANOSCOPE PURPOSE Read a Brticker Veeco Digital Instruments Nanoscope III AFM image CALLING SEQUENCE RD_NANOSCOPE
30. D models in TOPO using radially averaged PSD data can be used to define the PSD of a surface or interface in IMD Here s the TOPO_psd window after opening the radially averaged PSD data contained in the file topo examples PSD_r_example txt with the default Q v n fit and best fit parameter values displayed S TOPO PSD Analysis a File Preferences Units Precision A 14 e a gt D E b al L CO as E Ki a un L D I o a 2zr 27 20 20t7 1 oo Spatial Frequency f 1 A eflective rayOptics 23 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs 3 3 TOPO surf The TOPO surf program is used to analyze 2D surface profile data i e surface height Z as a function of surface position X and Y TOPO_surf can be run directly from TOPO Launcher or it can be run from the IDL command line using the syntax IDL gt topo_surf or if you have already defined X Y and Z IDL gt topo_surf x y Z Note The X and Y variables must be one dimensional arrays both defined in units of angstroms The Z variable must be a two dimensional array whose dimensions correspond to those of X and Y defined in units of angstroms When first starting TOPO_surf from TOPO Launcher or from the command line without passing X Y and Z values i e first command line example above you will be prompted to enter an IDL command to read sur
31. FLTARR 2 N_ELEMENTS ALPHA WAVES 0 LAMBDA 2 SIN DELTA 0 2 DTOR COS ALPHA DELTA 0 2 DTOR WAVES 1 LAMBDA 2 SIN DELTA 1 2 DTOR COS ALPHA DELTA 1 2 DTOR EXAMPLE Compute the range of spatial wavelengths in angstroms corresponding to scattering for 30 degree incidence with scattering angles from 1 to 60 degrees i e 30 1 to 30 60 for a photon wavelength of 100 angstroms ANGLE2WAVES 30 100 1 60 MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 eflective rayOptics 49 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 4 4 2 ANLZ_PROF NAME ANLZ_PROF PURPOSE Perform 2D analysis of X Y profile data This procedure combines the functionality of several TOPO routines and displays the results in a single composite plot using the PLOT_PROF PLOT_H_DIST PLOT_S_DIST PLOT_AUTOCOV and PLOT_PSD routines This routines is called by the TOPO_PROF widget application CATEGORY Topographic analysis CALLING SEQUENCE ANLZ_PROF X Y INPUTS X 1D array of equally spaced lengths in angstroms Y 1D array of heights in angstroms KEYWORD PARAMETERS PLOT A 4 element vector indicating which plots are to be made PLOT 0 Set to 1 to plot profile PLOT 1 Set to 1 to plot height and slope distributions PLOT 2 Set to 1 to plot autocovariance PLOT 3 Set to 1 to plot PSD XREGION 1D array o
32. N Integer specifying label position as per PLOT_TEXT Plus most IDL PLOT graphics keywords CTIONS The units for TAU and C must correspond to the values of the relevant tags of the common block variable TOPO That is set TOPO XUNITS_PTR to 0 for TAU in angstroms 1 for nm 2 for microns and 3 for mm Similarly set TOPO YUNITS_PTR to 0 for C in angstroms 2 1 for nm 2 2 for microns 2 and 3 for mm 2 The precision of the fit parameters that are labeled on the plot is determined by the values of the variables TOPO XPRECISION for length related parameters e g correlation length and TOPO YPRECISION for height related parameters e g rms roughness For example if TOPO XPRECISION 3 then three places to the right of the decimal will be displayed CATION HISTORY David L Windt Bell Laboratories May 1997 4 4 10 PLOT_H_DIST NAME PLOT_H DIST PURPOSE Procedure to compute plot and optionally fit a height histogram function CATEGORY Topographic analysis CALLING SEQUENCE PLOT_H_DIST X Y INPUTS X 1D array of lengths in units corresponding to the value of TOPO XUNITS_PTR Y 1D array of heights in units corresponding to the value of TOPO YUNITS_PTR KEYWORD PARAMETERS N_HEIGHTS Integer specifying the number of bins to be used in conjunction with the HISTOGRAM function HIST 1D output array of density values See the HISTOGRAM function HEIGHTS 1D output arra
33. O PLOT_S_DIST SE Procedure to compute plot and optionally fit a slope histogram function eflective rayOptics 61 7 October 2013 TOPO Version 2 2 CATEGORY Topographic analysis CALLING SEQUENCE PLOT_S_DIST X Y INPUTS X 1D array of lengths in units corresponding to the value of TOPO XUNITS_PTR Y 1D array of heights in units corresponding to the value of TOPO YUNITS_PTR KEYWORD PARAMETERS N_SLOPES Integer specifying the number of bins to be used in conjunction with the HISTOGRAM function HIST 1D output array of density values See the HISTOGRAM function SLOPES 1D output array of slope values the i th element of HIST is the density of slopes in the i th bin of SLOPES NOLABEL Set to inhibit labeling the SIGMA and L values LABEL_POSITION Integer specifying label position as per PLOT_TEXT Plus most IDL PLOT graphics keywords RESTRICTIONS The units for X and Y must correspond to the values of the relevant tags of the common block variable TOPO That is set TOPO XUNITS_PTR to 0 for X in angstroms 1 for nm 2 for microns and 3 for mm Similarly set TOPO YUNITS_PTR to 0 for Y in angstroms 1 for nm 2 for microns and 3 for mm The precision of the fit parameter i e rms slope that is labeled on the plot is determined by the value of the variable TOPO SPRECISION For example if TOPO SPRECISION 3 then three places to the right of the decimal will be displayed
34. OCOV_FIT NAME AUTOCOV_FIT PURPOSE Function to fit the autocovariance function with either a Gaussian and exponential or a Gaussian plus an exponential CATEGORY Topographic analysis CALLING SEQUENCE Result AUTOCOV_FIT TAU C PARS FIT FIT eflective rayOptics 52 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 TOPO User s Manual 4 TOPO for IDL Programmers INPUTS TAU 1D array of lag lengths C 1D array of autocovariance values FIT Set to 0 to fit to a Gaussian Set to 1 to fit to an exponential Set to 2 to fit to a Gaussiantexponential OUTPUTS Result Fit function PARS 1 D array of fit parameters PROCEDURE The autocovariance function is fit using either the GAUSS_FIT the EXPO_FIT or the GAUSSEXPO_FIT functions See the documentation for these functions in the windt library for a description of the elements of PARS MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 4 4 4 AUTOCOV2PARS NAME AUTOCOV2PARS PURPOSE Procedure to compute the rms roughness SIGMA and correlation length L from the autocovariance function C TAU CATEGORY Topographic analysis CALLING SEQUENCE AUTOCOV2PARS TAU C SIGMA L INPUTS TAU 1D array of lag lengths C 1D array of autocovariance values OUTPUTS SIGMA Rms roughness in units determined by the units of C For example if C nm 2 then SIGMA nm L Correlation length
35. TOPO Version 2 2 Installation Guide amp User s Manual 7 October 2013 Copyright 1997 2013 David L Windt davidwindt gmail com eflective rayOptics TOPO Version 2 2 Preface This document is the place to go for help with TOPO It is meant to be a combination Installation Manual Chapter 1 Quick Start Guide Chapter 2 Tutorial Chapter 3 and Reference Manual Chapter 4 with a few examples included in Chapter 3 to illustrate some of TOPO s capabilities TOPO was originally developed as a library of IDL routines to be used in your own IDL programs for analysis of measured 1D and 2D surface topography data obtained from optical surfaces This version of TOPO is focused principally on enhancements made since the last release to the user friendly programs included along with the TOPO IDL routines these programs are now called TOPO_prof TOPO_psd and TOPO_surf There s also a new program called TOPO Multiplot for analyzing one or more 2D surface data files Each of the user friendly programs use a graphical user interface GUI and can be run as is for example directly from the TOPO Launcher program for a variety of analyses of topography data without having to write new IDL programs hope you will read Chapters 1 and 2 of this document to get TOPO installed and running properly on your computer After that Chapter 3 of this document is a tutorial on the use of the GUI based TOPO routines with examples demo
36. TOPO User s Manual 3 TOPO Launcher Programs The TOPO Profile Analysis window is shown in Figure 1 as it appears just after opening the example file mentioned above E File Preferences Units Precision Iw Profile V Height Slope Distributions V Autocovariance V Power Spectral Density 1 0x10f Vit Bean Length x A HEIGHT DISTRIBUTION SLOPE DISTRIBUTION Ka e Hekri Oetrbution Tih Shape Oerbuticn T a 3 E H NET TEEN 4 2 D z ETA h DI AITEC ARANCE Aakeorvertires Ge 4 VON Lag Langth A POWER SPECTRAL DENSTY Figure 1 TOPO_prof window afte he example file described above eflective rayOptics 18 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs You can uncheck the boxes near the top of the TOPO Profile Analysis window to suppress display of any of the plots You can adjust the appearance of each plot and control how any fit may be displayed in that plot using the corresponding options in the Preferences menu For example here s the window that appears after selecting Preferences Power Spectral Density Frequency range 1 00 010 to 1 00 010 all Zero Padding Power Law Fit v X Min 0 Max o l Exact Iw Log Y Log The controls at top of this particular window are used to specify how the PSD is computed from the profile data i e frequency range used for PSD computation zero p
37. TOPO can be run using IDL version 6 3 or higher IDL is available for purchase from Exelis Visual Information Solutions http www exelisvis com ProductsServices IDL aspx NOTE The full version of IDL is required to run TOPO TOPO will NOT run using the free IDL Virtual Machine 1 1 2 Using TOPO as an XOP extension TOPO can be run as an extension to the free XOP software package available at ESRF http www esrf eu Instrumentation software data analysis xop2 3 If you will use TOPO as an XOP extension you can run the GUI based TOPO programs to analyze surface topography data You will not be able to use your own IDL programs containing TOPO routines however eflective rayUptics 6 7 October 2013 TOPO Version 2 2 TOPO Installation Guide 1 2 Installing TOPO as an IDL application If you will use TOPO as an XOP extension then you can skip this section and proceed to 1 3 Once you have IDL installed and running on your computer follow these steps to install and run TOPO 1 Create a directory folder called user_contrib in the main IDL installation directory NOTE You can install TOPO in a different directory if you so choose But if you do not install TOPO in the user_contrib directory as described here then you must edit the topo_cfg pro configuration file to specify the actual installation location See 1 4 1 for further details 2 Download the TOPO installation file topo_xxx tar gz from http www rxollc com
38. a file from big endian to little endian or visa versa Useful for reading on a Windows platform WYKO data files originally stored on Unix or Mac platforms or visa versa OUTPUTS X Vector of x position values in angstroms Y Vector of y position values in angstroms Z Array of height values in angstroms OPTIONAL OUTPUT PARAMETERS HEADER structure value containing the raw header information MODIFICATION HISTORY David L Windt Bell Laboratories March 1991 AKA RD_WYKO eflective rayOptics 43 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 TOPO User s Manual 4 TOPO for IDL Programmers August 1997 Added SWAP_ENDIAN keyword May 1998 Added SUB_TILT keyword 4 2 5 RD_ZYGO_NEWVIEW NAME RD_ZYGO_NEWVIEW PURPOSE Read a ZYGO NewView data file CALLING SEQUENCE RD_ZYGO_NEWVIEW FILE FILE X Y Z KEYWORD PARAMETERS FILE name of ZYGO data file TILT_SUB set to subtract tilt SPHERE_SUB set to subtract a 2nd order polynomial background HIST_EQUAL set to perform histogram equalization of image OUTPUTS X Vector of x position values in angstroms Y Vector of y position values in angstroms Z Array of height values in angstroms MODIFICATION HISTORY David L Windt Bell Laboratories June 1998 AKA RD_ZYGO 4 3 TOPO Launcher GUI Routines 4 3 1 TOPO_prof NAME TOPO_PROF PURPOSE A widget application for 1D profi
39. adding and windowing as per 84 4 16 and if a power law fit is displayed or not The controls at bottom are used to adjust the appearance of the plot Preferences windows associated with the other types of plots work similarly The Units menu on the main TOPO_prof window can be used to display lengths and or heights in units of nm um or mm while the Precision menu controls the number of digits displayed to the right of the decimal point for length height and slope parameters displayed on any plots Note that these settings are global and thus affect the display of any TOPO graphics not just those displayed in TOPO_prof The File gt 0Open menu option can be used to open a different data file in TOPO_prof You can export profile data as well as the computed height histogram slope histogram autocovariance function and PSD function using the corresponding File gt Export menu options You can print a hardcopy of the displayed graphics or print the graphics to a file using the File gt Print menu option For example you can print to a PostScript ps file which can then be converted to any number of other graphics file formats using freely available programs such as GhostScript ImageMagick etc or imported into vector graphics programs such as Corel Draw Adobe Illustrator etc for conversion and or further manipulation To illustrate shown in Figure 2 is a graphic that was made from a PostScript fil
40. and L Mattsson Introduction to surface roughness and scattering Optical Society of America 1989 E L Church Fractal surface finish Applied Optics 27 8 1518 1526 1988 pe Stearns Stochastic model for thin film growth and erosion Appl Phys Lett 62 1745 1747 1993 D K G de Boer X ray scattering and x ray fluorescence from materials with rough interfaces Phys Rev B 53 6048 6064 1996 eflective rayOptics 79 7 October 2013
41. bove can be used to create new tabs on the TOPO Multiplot window and each plot tab can display a different type of plot The example eflective rayOptics 31 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs TOPO Multiplot file topo examples topomultiplot_example_1_measurement tmp contains the same surface data we ve used in the example above and has been configured with four different plot tabs to illustrate some of TOPO Multiplot s visualization capabilities The tabs were also re named using the button labeled Rename To open this tmp file use the File gt 0Open menu option on the TOPO Multiplot menu bar The last three tabs are shown in the figures below r File Screen Color Units Precision 2D Contour 3D Surface Height Histogram Radially Averaged PSD Plot Type Height 3D Surface Plot Aray 1 xD dude FileName Date I XY TR Color Table al gt al gt Orientation about X Orientation about Z Title T Subtitle E Min 0 00000000 Max 0 00000000 C Exact Log Grid Title E Y Min f0 00000000 Max 0 00000000 M Exact Log Grid Tile E Z Min 0 00000000 Max 100 00000 Exact Log Title E Done Refresh Rename Add Plot Delete Plot Files eflective rayOptics 39 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO La
42. e that was created by printing from the TOPO_prof window shown eflective rayOptics 19 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs above in Figure 1 after suppressing the autocovariance and PSD plots in this example the PostScript file was imported into CorelDraw and then exported as a JPEG for import into the Word document used to create the PDF you are now reading PROFILE 6p A ET TT 4 Al 24 T Ka o O F 0 2 4 P V 10 18A r o 1 64A 7 6L_ i 0 0 0 5 1 0 1 5 2 0 Scan Length x um HEIGHT DISTRIBUTION SLOPE DISTRIBUTION 506 Krea Prorat KSE 80 EZ FEH i f h axg oto o f s axe 02o 0 1 06 A 0 0 61 deg 40 se E 30 5 a 3 l SZ S Q a 5 a 2 Ko o E Ko 10 O pao ds lidad d dp e i 6 4 2 0 2 4 6 4 2 0 2 4 Surface Height h A Surface Slope s deg Figure 2 Graphics produced using the File Print menu option from the TOPO_prof window shown in Figure 1 A PostScript file was created and then converted to JPEG using CorelDraw Reflective rayOptics 20 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs 3 2 TOPO_psd The TOPO_psd program is used to analyze 1D power spectral density PSD data i e S as a function of spatial frequency F TOPO_psd can be run directly from TOPO Launcher or it can be run from the IDL co
43. eoatven ce vanaduces aaiceeesoudceutsanieeeetanaiveeveaacess 72 4 428 SURE2PSD EE 73 4 4 29 TOPO Xe CONVERT riiisgte antaa aiaa sacsdudenstacd diari late 75 44 30 TOPO e elt TEE 75 5 Performance and Troubleshooting cccceessssccecececsssesnnaecececeeesseceaecececssseseaeaeseeecesseseaeaeeeeseeeeeees 77 5 1 Frequently Asked Questions cccceessscecececesseseaesecececesseseaseseceeecesseseaaeseeeescessuseuaeseeeessessnsaaeess 77 5 1 1 Q I can t get TOPO to work start ccccsccccssecesssccssseceseceeseeceseeccsaeeecssecesseeessteseaeeesaeeeeees 77 5 1 2 Q Can get a copy of the TOPO source code 77 5 1 3 Q Will can you include feature X in a future release Of TOPO cccccssecssseeesseceeeeeeees 77 5 1 4 Q Will TOPO work with the free IDL Virtual Machine 77 5 2 Reportine BULA diia 17 6 Ee 79 eflective rayOptics 5 7 October 2013 TOPO Version 2 2 1 Installing TOPO 1 1 System Requirements TOPO is written in the IDL scientific programming language and will run on any platform supported by IDL While most TOPO routines are intended for use in your own IDL programs the GUI based programs included with TOPO TOPO_prof TOPO_psd TOPO_surf and TOPO Multiplot require little or no IDL expertise There are two ways to run TOPO 1 using a licensed copy of IDL and 2 using the free XOP package which includes an embedded licensed copy of IDL 1 1 1 Using TOPO as an IDL application
44. er of zero height points to add on either side of the profile data HANNING Set this to use a Hanning window function KAISER Set this to use a Kaiser Bessel window function RESTRICTIONS eflective rayOptics 64 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 The X values must be equally spaced PROCEDURE S Length ABS FFT Y Window 1 2 Where Length is as described above and Window is the value of the optional window function Hanning or Kaiser Bessel MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 windt astro columbia edu Nov 1998 When using the HANNING or KAISER keywords the window function is now normalized so that the integral of the PSD is constant i e independent of your choice of window September 2000 Corrected a problem wherein the spatial frequencies were computed incorrectly 4 4 17 PROF2SLOPE NAME PROF2SLOPE PURPOSE Function to compute the slope from the profile data CATEGORY Topographic analysis CALLING SEQUENCE Result PROF2SLOPE X Y INPUTS X 1D array of equally spaced lengths Y 1D array of heights OUTPUTS Result 1D array of slope values in degrees RESTRICTIONS The X values must be equally spaced X and Y must have the same units MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 4 4 18 PSD_FIT NAME PSD_FIT PURPOSE eflective rayOptics 65 TOPO User s Manual
45. er you ve configured TOPO Multiplot to your liking you can save the results to a tmp file using the File gt Save menu option Note When you save a TOPO Multiplot file all surface data loaded into TOPO Multiplot are included in the tmp file The File gt Print menu option can be used to print a hardcopy of each plot tab You can also print to a PostScript file to create graphics that can be used for presentations or publications For example 40 O TTTTTT TT TTTTTT TTT TTT TTTTTTT Sample A ed 3 7 28 2 Sample B 2013 7 28 K Z 10 D gt L a O E T 10 o 0 E E BS g 3 10 A 10 paa tales Lag l Al LL oe 0 01 0 10 1 00 10 00 100 00 1000 00 Spatial Frequency f 1 um Figure 4 Graphics produced using the File gt Print menu option from the TOPO Multiplot window shown in the previous figure a PostScript file was created and then converted to JPEG using CorelDraw eflective rayOptics 38 7 October 2013 TOPO Version 2 2 4 TOPO for IDL Programmers 4 1 TOPO Common Block Variables If you are using TOPO as an IDL application then you will have started TOPO at the IDL command line using run topo as explained in Chapter 2 Some TOPO routines use IDL common block variables which are defined and accessible at the command line when you run topo pro this way Almost none of these common block variables should be
46. f radially averaged PSD values eflective rayOptics 67 7 October 2013 TOPO Version 2 2 CATEGORY Topographic analysis CALLING SEQUENCE Result PSD_SIGMA_XI_H_FIT F S PARS INPUTS F 1D array of spatial frequencies S 1D array of power spectral density values OUTPUTS Result Fit function PARS 1 D array of fit parameters sigma xi H KEYWORD PARAMETERS RANGE 2 element array of min and max spatial frequencies to be used for fitting Default is to use the entire range of data FFIT Array of F values corresponding to the range used for fitting RESTRICTIONS F and S must use the same length units MODIFICATION HISTORY David L Windt Bell Laboratories May 1998 4 4 21 PSD2AUTOCOV NAME PSD2AUTOCOV PURPOSE Procedure to compute the autocovariance function from the power spectral density function S F CATEGORY Topographic analysis CALLING SEQUENCE PSD2AUTOCOV FX FY S TAUX TAUX TAUY TAUY INPUTS FX 1D array of spatial frequencies along X direction FY Optional 1D array of spatial frequencies along Y direction S 2D array of power spectral density values KEYWORD PARAMETERS eflective rayOptics 68 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 TOPO User s Manual 4 TOPO for IDL Programmers TAUX TAUY Lag length vectors along X and Y OUTPUTS C TAUX TAUY Autocovariance function PROCEDURE C is computed from
47. f subscripts for X specifying a region of interest SUB_TILT Set to subtract tilt using SUB_TILT HEIGHTS Output array of heights see HEIGHT_DIST in units determined by the value of TOPO YUNITS_PTR see PROCEDURE below HEIGHT_HIST Output array of height histogram values See HEIGHT_DIST N_HEIGHTS Number of heights to be used for HEIGHT_DIST NOFIT_HEIGHT Set to inhibit fitting the height histogram with a Gaussian SLOPES Output array of slopes in degrees See HEIGHT_DIST SLOPE_HIST Output array of slope histogram values See HEIGHT_DIST N_SLOPES Number of slopes to be used for HEIGHT_DIST eflective rayOptics 50 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 TOPO User s Manual 4 TOPO for IDL Programmers NOFIT_SLOPE Set to inhibit fitting the height histogram with a Gaussian TAU Output array of lag lengths in units determined by the value of TOPO XUNITS_PTR see PROCEDURE below AUTOCOV Output array of autocovariance values in units determined by the value of TOPO YUNITS_PTR see PROCEDURE below For example if TOPO YUNITS_PTR 1 then the AUTOCOV units will be nm 2 FIT_AUTOCOV Same as FIT_TYPE keyword to PLOT_AUTOCOV FREQ Output array of spatial frequencies in units determined by the value of TOPO XUNITS_PTR see PROCEDURE below For example if TOPO XUNITS_PTR 1 then the FREQ units will be 1 nm PSD Output array
48. face data stored in a file so as to define the X Y and Z arrays IDL command to read surface data file rd_nanoscope x y z Cancel ox The default command to read 2D profile data in TOPO_surf is RD_NANOSCOPE which can be used to read an AFM image created by the Brucker Veeco Digital Instruments Nanoscope lll instrument as described in detail in 4 2 3 Other routines built in to TOPO for reading surface profile data files are described in 4 2 Alternatively you can use your own IDL programs to read 1D profile data by entering the corresponding IDL commands using valid IDL syntax to define the variables X Y and Z into the text box in the figure shown above Compound IDL commands i e using the amp symbol are allowed To illustrate we ll use the default RD_NANOSCOPE routine to open the 2D surface data file topo examples nanoscope_example_6_v_0x05120005 dat that is included with the TOPO distribution IDL Programmers should consult 4 3 3 for more information on the TOPO_surf routine eflective rayUptics 24 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs Organize v New folder Name Date modified Favorites HE Desktop _ micromap_example dat 3 L windt NASI N _ nanoscope_example_1_v_0x04220202 dat 5 15 19 12 AM 36 KB DAT File A windt linux _ nanoscope_example_2_v_0x04220202 dat 5 1 d 36KB DAT File server NASI _ nanoscope_example_3_
49. for mm The precision of the fit parameters that are labelled on the plots is determined by the values of the variables eflective rayOptics 47 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 TOPO User s Manual 4 3 4 NAME 4 TOPO for IDL Programmers TOPO XPRECISION for length related parameters e g correlation length TOPO YPRECISION for height related parameters e g rms roughness and TOPO SPRECISION for slope related parameters e g rms slope For example if TOPO XPRECISION 3 then three places to the right of the decimal will be displayed The TOPO UNITS_PTR and TOPO PRECISION variables can either be set explicitly before executing this procedure or they can be set transparently to the user be selecting the appropriate menu items once the procedure is running If no data are passed the user is prompted to enter the IDL command string used to read in new data This command string must explicitly define X Y and Z For example if you re reading in Nanoscope AFM data you can use the RD_NANOSCOPE procedure as in RD_NANOSCOPE X Y Z FILE MyProfile dat You might also try other programs described in 4 2 to import surface data If you cannot use RD_WYKO or RD_DIGITAL_AFM then will need to write your own IDL procedure to read in the data with X Y and Z as explicit parameters i e MY_PROCEDURE X Y Z or Result MY_FUNCTION X Y Z TOPO Multiplot
50. h for your support also wish to thank to all the TOPO users who have provided to me valuable feedback and suggestions eflective rayOptics 2 7 October 2013 TOPO Version 2 2 TOPO Version 2 2 Installation Guide amp User s Manual Contents L Installing TOPO iii A A did 6 1 1 Ag 6 1 1 1 Using TOPO as an IDL application ccccccccccecesssssseeececeesesesneaeceeecesseseeaeaeeeeeeesecssaeaeseeseesees 6 1 1 2 Using TOPO as an XOP exvtension 6 1 2 Installing TOPO as an IDL application 7 1 3 Installing TOPO as an XOP evtenslon occccconononocncnnonoconononononononnnnnononnnnnnnnnnnnnnnnnnonnnnnnnnnnnnonnnnnnnnos 10 1 4 Customizing the TOPO installation topo_cfg Dro 12 1 4 1 Non standard installation location 2 0 0 ceecceeeseceesseceeececeeeeeeeaeeeeaaeceeaeeceeeeessaeeeeaaeeeeeeeenaees 12 1 4 2 Other customizable settings cional dal el dica 12 1 5 Common Installation Problems and Solutions 13 2 USING TOPO o adora ainia 14 2 1 Overview What is TOPO and what can it dod nn nana ncnnncnnns 14 2 2 Starting TOPO 0 a RM ae ee 15 3 TOPO Launcher Programs eats vbeagesavaiceced ase sdeaulinneaduvesstanetedeeeadtoesgeantinnesdavinnas 16 3 1 TOPO DO E 16 3 2 TOPO o E 21 3 3 TOPO SUF WEE 24 34 TOPO MUTI POE E 27 4 TOPO for IDLProgramMerS irissen aceea seresa da 39 4 1 TOPO Common Block Variables siiani aeae ariadna 39 4 2 BER 40 4 2 1 ERO Miss Aide e dilata 40 eflective rayOptics 3 7 October 2013 TOPO Version 2
51. he TOPO library that can be used to read topography data files are also described in Chapter 4 Note The File gt Change Working Directory menu option in TOPO Launcher allows you to globally change the working directory It is equivalent to using the IDL cd command at the IDL prompt 3 1 TOPO_prof The TOPO_prof program is used to analyze 1D surface profile data i e surface height Y as a function of surface position X TOPO_prof can be run directly from TOPO Launcher or it can be run from the IDL command line using the syntax IDL gt topo_prof Or if you have already defined X and Y IDL gt topo_prof x y Note The X and Y variables must be one dimensional arrays of equal length both defined in units of angstroms The X values also must be equally spaced When first starting TOPO_prof from TOPO Launcher or from the command line without passing X and Y values i e first command line example above you will be prompted to enter an IDL command to read profile data stored in a file so as to define the X and Y arrays TOPO_prof is essentially a wrapper for the ANLZ_PROF routine described in 4 4 2 IDL Programmers should consult 84 3 1 for more information on the TOPO_ prof routine eflective rayOptics 16 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs IDL command to read profile data file erom xy Caneel OK The default command to read 1D profile da
52. he free IDL Virtual Machine A Unfortunately no TOPO makes extensive use of the IDL execute function which is explicitly excluded from the Virtual Machine 5 2 Reporting Bugs While there are almost certainly programming errors in the TOPO source code that remain undetected at the time of this release TOPO is supposed to be resilient to such problems Nevertheless nobody s perfect So if you do find a situation where TOPO stops working I d like to know about it Please contact me with as much detail as you can provide exactly what you were doing exactly what happened etc if you can send a faulty file that would help greatly Meanwhile the simplest work around for you if TOPO stops working assuming that you re using TOPO as an IDL application is to exit IDL and start over Or you can try typing the command retall at the IDL prompt and see if TOPO comes back to life If you encounter a fatal error using TOPO as an XOP eflective rayOptics 77 7 October 2013 TOPO Version 2 2 TOPO User s Manual 5 Performance and Troubleshooting extension the program will probably just exit completely perhaps with an error message that you can report to me davidwindt gmail com Also check out the IMD amp TOPO Google group https groups google com forum forum imd_topo for discussion and announcements of future releases eflective rayOptics 78 7 October 2013 TOPO Version 2 2 6 References 1J M Bennett
53. ht and or don t look much like the examples in this document Solution The fonts used by TOPO which are specified in the topo_cfg pro configuration file might not be available on your computer Edit the topo_cfg pro file as described in 1 4 and specify valid fonts that are actually installed on your computer Problem Special characters such as A uw 6 etc don t display correctly in the TOPO windows Solution The special character codes for your particular installation which are specified in the topo_cfg pro configuration file must be the correct codes for the fonts used by TOPO which are also specified in that file Edit the topo_cfg pro file as described in 1 4 and specify valid special character codes for the fonts that you have specified If your operating system is not specifically listed in the topo_cfg pro configuration file you ll need to manually add the necessary entries for optical constants and atomic scattering factors directories fonts etc using as a template the lines in that file that contain YOUR OS replace YOUR OS with the value of the IDL system variable version os as defined on your computer eflective rayOptics 13 7 October 2013 TOPO Version 2 2 2 Using TOPO 2 1 Overview What is TOPO and what can it do The TOPO software package comprises a library of IDL routines for analysis of measured 1D or 2D surface topography data such as that obta
54. ined by atomic force microscopy AFM optical profilometry or any other type of contact or non contact surface profile measurement technique The TOPO routines are largely based on the work by Bennet and Mattsson and Church and you are strongly encouraged to read the material in those references only minimal discussion is included in this document of the concepts behind the TOPO surface topography analysis routines The TOPO IDL routines can be used in your own IDL programs if you are running TOPO as an IDL application TOPO also includes four user friendly programs each with a graphical user interface GUI TOPO_prof for analysis of 1D surface height profile data TOPO_psd for analysis of 1D power spectral density PSD data TOPO_surf for analysis of 2D surface height data and TOPO Multiplot for analysis of one or more 2D surface height data sets The TOPO GUI programs can be executed from TOPO Launcher or from the IDL command line if you are use TOPO as an IDL application eflective rayUptics 14 7 October 2013 TOPO Version 2 2 2 2 Starting TOPO TOPO User s Manual Follow the instructions in Chapter 1 to install TOPO on your computer To start TOPO follow these steps as appropriate for your installation Operating System IDL or XOP Linux Mac OS X a XOP Solaris Windows Starting IMD Start IDL and then type IDI rtm 19 You can also re start TOPO Launcher by typing topo_launcher at the prom
55. ith the windt library at www rxollc com idl The source code for the remaining data importing routines described here is included in the t opo readers directory 4 2 1 EROM NAME EROM PURPOSE Read columns of data from a text file This program can be used to read data written by the MORE program The file to be read must be such that if the data are space separated then all variables are numeric String variables are allowed only if the data are separated by tabs colons etc The file may contain any number of comment lines which MUST begin with a semicolon and MUST be positioned before all data lines CALLING SEQUENCE EROM VO V1 V2 V9 or EROM V V KEYWORD PARAMETERS V Set this keyword to a named variable that will be returned as an array of structures holding the data and the variable names specified in the last comment line See RESTRICTIONS below for more details FILE String specifying the name of a file if not supplied the user is queried SKIP The number of lines at the beginning of the file that should be skipped TAB Specify TAB for tab separated data The default is space separated data It is only necessary to specify this keyword if the file contains any string data columns SEPARATOR A string specifying the character separating the data columns eflective rayOptics 40 7 October 2013 TOPO Version 2 2 COMMENT Set this keyword to a named variable that
56. le analysis This program is a widget interface to the ANLZ_PROF routine CATEGORY Topographic analysis CALLING SEQUENCE TOPO_PROF X Y GROUP GROUP OPTIONAL INPUTS X 1D array of equally spaced lengths in angstroms eflective rayOptics 44 7 October 2013 TOPO Version 2 2 Y 1D array of heights in angstroms KEYWORD PARAMETERS GROUP Widget GROUP_LEADER keyword to XMANAGER COMMON BLOCKS COMMON TOPO COMMON PLOT_PRINT RESTRICTIONS The X values must be equally spaced X and Y must be in angstroms PROCEDURE Although X and Y must be in angstroms the units for displayed variables are determined by the values of the relevant tags of the common block variable TOPO That is set TOPO XUNITS_PTR to 0 for angstroms 1 for nm 2 for microns and 3 for mm Same goes for TOPO YUNITS_PTR The precision of the fit parameters that are labeled on the plots is determined by the values of the variables TOPO XPRECISION for length related parameters e g correlation length TOPO YPRECISION for height related parameters e g rms roughness and TOPO SPRECISION for slope related parameters e g rms slope For example if TOPO XPRECISION 3 then three places to the right of the decimal will be displayed The TOPO UNITS_PTR and TOPO PRECISION variables can either be set explicitly before executing this procedure or they can be set transparently to the user be selecting the appropriate menu items once
57. lor Units Precision 10 Power Spectral Density S f 4 107 0 01 0 10 1 00 10 00 106 00 10G0 0 Spatial Frequency f D dm Q Pt Type PSD Radially Average D Legend L Mio Include File Name Y Date I XY TC RPhi I Condensed by Color y PSD Ft None DI o Er X Min 0 00000000 Max 0 00000000 Exact M Log W Gid Tile Y Min 0 00000000 Max 0 00000000 TC Exact M log Em Tile E min 0 00000000 max 0 00000000 M Exact I Log SH We ve checked the box labeled Condensed in the last figure above this causes the plot legend to display just a single line for Sample A and a single line for Sample in blue in pink respectively If the Condensed box is unchecked the legend would include a line for each of the 4 files included in the list shown in the TOPO Multiplot Files window That might be useful in this particular example to distinguish between the 2 um and 10 um scans as well as the sample IDs if we had configured the 2 um scans to display using other colors or dotted lines perhaps We ve also checked the Date box in the above example which causes the measurement dates to be included in the legend If you specify X Y or R Phi location values for each file these values can also be included in the legend by checking the corresponding boxes Reflective rayOptics 37 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs Aft
58. m spatial frequency along X or Y whichever is smallest The i th value of SR at a specific FR i is equal to the average of all S values contained in the annulus defined by FR i 5 DFR lt sqrt FX 2 FY 2 lt FR i 5 DFR where DFR is the spatial frequency increment MODIFICATION HISTORY David L Windt Bell Laboratories May 1998 windt astro columbia edu September 2000 Corrected some problems with the way SR and FR were computed that arose when FX and FY are unequal Eric Gullikson LBL EMGullikson lbl gov 4 4 24 PSDPARS_ANGLE2SIGMA_L NAME PSDPARS_ANGLE2SIGMA_L PURPOSE Function to compute the rms roughness SIGMA and correlation length L from a the maximum spatial wavelength corresponding to scattering for incidence angle ALPHA wavelength LAMBDA into scattering angles ALPHA DELTA 0 to ALPHA DELTA 1 and b the power law parameters K_N and N CATEGORY Topographic analysis CALLING SEQUENCE PSDPARS_ANGLE2SIGMA_L K_N N ALPHA LAMBDA DELTA SIGMA L INPUTS K_N Power law scaling factor eflective rayOptics 70 7 October 2013 TOPO Version 2 2 N Power law exponent ALPHA A scalar or 1D array of incidence angles LAMBDA Scalar specifying the incidence wavelength DELTA 2 element array specifying the min and max scattering angles to consider OUTPUTS SIGMA Rms roughness L Correlation length PROCEDURE The ANGLE2WAVES procedure is used to compute the range of spa
59. mmand line using the syntax IDL gt topo_psd or if you have already defined F and S IDL gt topo_psd f s Note S and F must be one dimensional arrays of equal length S has units of while F has units 1 A When first starting TOPO_psd from TOPO Launcher or from the command line without passing F and S values i e first command line example above you will be prompted to enter an IDL command to read profile data stored ina file so as to define the F and S arrays IDL command to read profile data file leromf s Cancel ox The default command to read 1D PSD data in TOPO_psd is EROM which can be used to read plain text files as described in detail in 4 2 1 Alternatively you can use your own IDL programs to read 1D profile data by entering the corresponding IDL commands using valid IDL syntax to define the variables F and S into the text box in the figure shown above Compound IDL commands e using the amp symbol are allowed If you use the default command erom f s to read a plain text file i e containing two columns of data F and S you will then be prompted to select the name of the file to read To illustrate we ll open the 1D PSD data file topo examples PSD_x_example txt that is included with the TOPO distribution After opening the surface profile data file the TOPO PSD Analysis window displays by default the data and a power law fit described in Church 2
60. name Add Plot Each 2D surface data file to be included for display in TOPO Multiplot must be added one at a time Click on the little Files button at the bottom of the TOPO Multiplot window circled in red in the figure above to open the TOPO Multiplot Files window associated with this instance of TOPO Multiplot shown in the next figure eflective rayOptics 27 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs T Only use surface data between z 0 000000 and 0 000000 A 0 PSD Computation 4 p No Window _y bm hla il Zero Padding T Only use PSD data between f 0 000000 and 0 000000 1 4 Re Compute Statistics P 10 0000000 AT RMS Position d 0 000000 mm 0 000000 mm F 0 000000 mm Phi 0 000000 deg To add a new surface data file click the Add File button circled in red above We ve already clicked it in the figure above Then enter the IDL command to read the data file in the text box labeled IDL Read Command You can use one of the routines described in 4 2 or your own IDL routines if running TOPO as an IDL application Specify the name of the file to read in the text box labeled File Click the button labeled Read to import the file TOPO Multiplot will read the data file specified and also compute the height histogram the 2D PSD the 1D radially averaged PSD and the 1D X and Y averaged PSDs To illustrate Fig
61. nstrating some of their capabilities while Chapter 4 is a reference manual for the TOPO IDL routines that you can use in your own IDL programs Also check out the IMD amp TOPO Google group https groups google com forum forum imd_ topo for discussion and announcements of future releases A note about notation Throughout this manual computer file names are always written in this font When files are written with their full path or sometimes even with a partial path as in the very next sentence l Il use notation applicable to unix i e linux Mac OS X and Solaris operating systems using a forward slash to delineate subdirectory names For example topo examples which means the examples subdirectory in the topo installation directory the leading means wherever the topo installation directory is installed on your computer Of course Microsoft Windows platforms use the backward slash as in topo examples so if you re using a Windows computer please substitute backward slashes for forward slashes when you see a file name with a forward slash in this document Acknowledgements The on going development of TOPO has been made possible in large part by continual support from NASA since 1999 for high energy astrophysics technology development most recently under NASA grant number NNX13AC54G To all the NASA people involved and the proposal review panels over the years can t thank you enoug
62. nt array specifying YTYPE YRANGE 0 YRANGE 1 YSTYLE profile plot keywords for AYAXIS 4 element array specifying YTYPE YRANGE 0 YRANGE 1 YSTYLE autocovariance plot keywords for PYAXIS 4 element array specifying YTYPE YRANGE 0 YRANGE 1 YSTYLE plot keywords for PSD RESTRICTIONS The X values must be equally spaced X and Y must be in angstroms PROCEDURE Although X and Y must be in angstroms the units for displayed and returned keyword variables are determined by the values of the relevant tags of the common block variable TOPO That is for microns set TOPO XUNITS_PTR to 0 for angstroms 1 for nm 2 and 3 for mm Same goes for TOPO YUNITS_PTR The precision of the fit parameters that are labeled on the plots is determined by the values of the variables TOPO XPRECISION for length related parameters e g correlation length TOPO YPRECISION for height related parameters e g rms roughness and TOPO SPRECISION for slope related parameters e g rms slope For example TOPO XPRECISION 3 then three places to the right of the decimal will be displayed if MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 January 1998 Added call to TEK_COLOR unless D NAME eq HP and when D NAME eq CGM set the color index for p color to black May 1998 Added PLOT keyword August 2013 Replaced call to TEK_COLOR with call to RXO_COLOR 4 4 3 AUT
63. ocovariance function CATEGORY Topographic analysis CALLING SEQUENCE PLOT_AUTOCOV TAUX TAUY C INPUTS TAUX 1D array of lag lengths along X direction in units corresponding to the value of TOPO XUNITS_PTR TAUY 1D array of lag lengths along Y direction in units corresponding to the value of TOPO YUNITS_PTR C 1D array of autocovariance values in units corresponding to the value of TOPO YUNITS_PTR KEYWORD PARAMETERS SIGMA Output rms roughness computed from C using AUTOCOV2PARS in units corresponding to the value of TOPO YUNITS_PTR CORR_LENGTH Correlation length computed from C using AUTOCOV2PARS in units corresponding to the value of TOPO XUNITS_PTR FIT_TYPE Set to 1 for no fit 0 for Gaussian fit 1 for exponential fit 2 for Gaussiant exponential fit REGION Set to interactively select a region of interest for fitting using GET_ROI CFIT Output fit dependent variable TAUFIT Output fit independent variable FIT_PARS Fit parameters See AUTOCOV_FIT FIT_COLOR IDL graphics keyword for fit function FIT_THICK IDL graphics keyword for fit function FIT_LINESTYLE IDL graphics keyword for fit function NOLABEL Set to inhibit labeling the SIGMA L and fit parameters values eflective rayOptics 57 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 TOPO User s Manual RESTR MODIF 4 TOPO for IDL Programmers LABEL_ POSITIO
64. of power spectral density values in units determined by the value of TOPO YUNITS_PTR see PROCEDURE below For example if TOPO YUNITS_PTR 1 then the PSD units will be nm 3 ZERO_PAD See PROF2PSD HANNING See PROF2PSD KAISER See PROF2PSD RANGE See PROF2PSD FIT_PSD Same as FIT_TYPE keyword to PLOT_PSD Z_VALUE Z parameter needed for Omega nu n PSD fits PRSTYLE 5 element array specifying COLOR LINESTYLE THICK PSYM SYMSIZE keywords for profile plot except that PSYM and SYMSIZE are ignored HSTYLE 5 element array specifying COLOR LINESTYLE THICK PSYM SYMSIZE keywords for height histogram plot except that PSYM and SYMSIZE are ignored SSTYLE 5 element array specifying COLOR LINESTYLE THICK PSYM SYMSIZE keywords for slope histogram plot except that PSYM and SYMSIZE are ignored ASTYLE 5 element array specifying COLOR LINESTYLE THICK PSYM SYMSIZE keywords for autocovariance plot PSTYLE 5 element array specifying COLOR LINESTYLE THICK PSYM SYMSIZE keywords for PSD plot PRXAXIS 4 element array specifying XTYPE XRANGE 0 XRANGE 1 XSTYLE keywords for profile plot AXAXIS 4 element array specifying XTYPE XRANGE 0 XRANGE 1 XSTYLE keywords for autocovariance plot PXAXIS 4 element array specifying XTYPE XRANGE 0 XRANGE 1 XSTYLE keywords for PSD plot eflective rayOptics 51 7 October 2013 TOPO Version 2 2 PRYAXIS 4 eleme
65. pt IMD gt topo_launcher At the command line type S xop topo4xop Or type S xop and then XOP gt Load extension and then select topo4xop from the list of installed extensions and then click Accept Double click C xop2 3 topo4xop vbs If that doesn t work Double click C xop2 3 topo4xop bat If neither method works edit topo4xop bat and check that the specified path to xop bat is correct for your installation Or start XOP as per the XOP instructions and then XOP gt Load extension and then select topo4xop from the list of installed extensions and then click Accept l Replace C xop2 3 with your actual XOP installation directory eflective rayOptics 15 7 October 2013 TOPO Version 2 2 3 TOPO Launcher Programs This chapter is meant to be a brief tutorial on the stand alone user friendly programs included in the TOPO library that can be run from TOPO Launcher These programs also can be run directly from the IDL command line or called from your own IDL programs if you are running TOPO as an IDL application There is no limit on the number of instances of any of these programs that can be opened simultaneously Detailed reference information for IDL programmers regarding the TOPO Launcher routines described in this chapter along with reference information on the underlying TOPO IDL routines used by these programs is presented Chapter 4 The routines included in t
66. r mm TOPO YUNITS_PTR An integer that defines the height units for displayed variables Set this variable to O for angstroms 1 for nm 2 for microns and 3 for mm The precisions with which best fit parameters and other quantities e g RMS roughness etc are displayed are controlled by the TOPO XPRECISION TOPO YPRECISION and TOPO SPRECISION structure tags TOPO XPRECISION An integer that defines the number of digits displayed to the right of the decimal point for length related parameters e g correlation length TOPO YPRECISION An integer that defines the number of digits displayed to the right of the decimal point for height related parameters e g RMS roughness eflective rayOptics 39 7 October 2013 TOPO Version 2 2 TOPO User s Manual 4 TOPO for IDL Programmers TOPO SPRECISION An integer that defines the number of digits displayed to the right of the decimal point for slope related parameters e g RMS slope 4 2 Data Importing Routines The IDL routines described in this section can be used to read 1D or 2D surface data files in TOPO You can also use your own IDL programs to read surface data files if you are using TOPO as an IDL application If you are using TOPO as an extension to XOP then these are likely to be the only routines you can use to import your measured surface data The source code for the EROM procedure is included w
67. sed to analyze and compare data from multiple surface data files Add as many 2D surface profile files as you like be sure to click the Read button after making any changes to the file the Z limits or the PSD settings Note that the histogram and PSD functions are only computed once when the file is read i e when you click the Read button To illustrate use the File gt 0Open menu option in TOPO Multiplot to open the example tmp file tmp examples topomultiplot_example_4_measurements tmp which contains four AFM images from two different samples each sample was measured over 2 um and 10 um scan lengths x ua a IDL Read Command r_nanoscope xy z tilt sphere Read bo File ltopomultiplot example_image_A_2um dat els 2 0000000x2 0000000 um Measured Sun Jul 28 16 46 18 2013 Only use surface data between 2 15 3437 and 18 9303 A PSD Computation a j No Window Je bas Ex Ev kl Zero Padding I Only use PSD data between f 0 499021 and 127 750 14m Re Compute Statistics P V 34 273968 Y RMS Position X 0 000000 mm Y 0 000000 mm R 0 000000 mm Phi 0 000000 deg We ve used the Label text box in the TOPO Multiplot Files window to indicate that the first two files correspond to Sample A and the last two to Sample B these labels can be used in TOPO Multiplot graphics We ve also selected the same plot styles for the two Sample
68. ta in TOPO_prof is EROM which can be used to read plain text files as described in detail in 4 2 1 Alternatively you can use your own IDL programs to read 1D profile data by entering the corresponding IDL commands using valid IDL syntax to define the variables X and Y into the text box in the figure shown above Compound IDL commands e using the amp symbol are allowed If you use the default command erom x y to read a plain text file i e containing two columns of data X and Y you will then be prompted to select the name of the file to read To illustrate we ll open the 1D profile data file topo examples profile_data_example txt that is included with the TOPO distribution Organize y New folder Lo System Volume Information A Temp A Users Name Date modified 5 30 1998 10 42 AM 5 15 1998 11 42 AM 515 KB 136 KB DAT File DAT File _ micromap_example dat _ nanoscope_example_1_v_0x04220202 dat A xop2 3 Le bin86 B data A doc A examples A extensions J idi70win A ifc Ak o modules J tmp wm Removable Disk D 43 DVD RW Drive E Li media NAS1 M de Windows L _ nanoscope_example_2_v_0x04220202 dat _ nanoscope_example_3_v_0x04100200 dat _ nanoscope_example_4_v_0x04400003 dat _ nanoscope_example_5_v_0x04100200 dat _ nanoscope_example_6_v_0x05120005 dat 5 17 1998 6 05 PM 5 18 1998 9 00 PM 10 6 1998 4 46 PM 8 19 2005 9 34 AM 8 19 20
69. the FFT of S MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 4 4 22 PSD2PARS NAME PSD2PARS PURPOSE Procedure to compute the rms roughness SIGMA and correlation length L from the power spectral density function S F CATEGORY Topographic analysis CALLING SEQUENCE PSD2PARS F S SIGMA L INPUTS F 1D array of spatial frequencies S 1D array of power spectral density values OUTPUTS SIGMA Rms roughness in units of S 1 3 L Correlation length in units of 1 F PROCEDURE SIGMA SQRT 2 Integral S L 1 2 SIGMA 4 Integral S 2 MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 4 4 23 PSD2RAVEPSD NAME PSD2RAVEPSD PURPOSE Function to compute the radially averaged PSD from a 2D PSD array CATEGORY eflective rayOptics 69 7 October 2013 TOPO Version 2 2 TOPO User s Manual 4 TOPO for IDL Programmers Topographic analysis CALLING SEQUENCE SR PSD2RAVEPSD FX FY S FR FR INPUTS FX 1D array of spatial frequencies along X direction FY Optional 1D array of spatial frequencies along Y direction S 2D array of power spectral density values OUTPUTS SR 1D array of radially averaged PSD values FR 1D array of spatial frequencies PROCEDURE The radially averaged PSD is computed for a vector of FR values with FR sqrt FX 2 FY 2 and for FR values ranging from the minimum spatial frequency to the maximu
70. the procedure is running If no data are passed the user is prompted to enter the IDL command string used to read in new data This command string must explicitly define X and Y in angstroms For example if your data is in the form of a plain text file consisting of two columns of data X and Y then you can use the default EROM routine as in EROM X Y FILE MyProfile dat If your data is not in this form then you will probably need to write your own IDL procedure to read in the data with X and Y as explicit parameters i e MY_PROCEDURE X Y or Result MY_FUNCTION X Y Once the profile data are defined this routine uses the ANLZ_PROF routine to compute the height distribution the slope distribution the autocovariance and the power spectral density with optional fitting and displays the results in a composite plot that can be printed using PLOT_PRINT Various popup widgets are used to adjust the computations fits and plots to the users preference eflective rayOptics 45 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 4 3 2 TOPO_psd NAME TOPO_PSD PURPOSE A widget application for 1D PSD analysis This program is a widget interface to the PLOT_PSD routine CATEGORY Topographic analysis CALLING SEQUENCE TOPO_PSD F S GROUP GROUP OPTIONAL INPUTS F 1D array of spatial frequencies in 1 angstroms S 1D array of power spectral density values
71. tial wavelengths corresponding to scattering at incidence angle ALPHA wavelength LAMBDA into scattering angles ALPHA DELTA i The maximum wavelength is then used along with the specified K_N and N to compute SIGMA and L using the PSDPARS2SIGMA_L routine MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 4 4 25 PSDPARS2SIGMA_L NAME PSDPARS2SIGMA_L PURPOSE Procedure to compute the rms roughness SIGMA and correlation length L from the scan LENGTH and the power law parameters K_N and N CATEGORY Topographic analysis CALLING SEQUENCE PSDPARS2SIGMA_L K_N N LENGTH SIGMA L INPUTS K_N Power law scaling factor N Power law exponent LENGTH Scan length OUTPUTS SIGMA Rms roughness L Correlation length PROCEDURE SIGMA SORT K_n LENGTH N 1 N 1 L N 1 2 LENGTH 2 2 N 1 eflective rayOptics 71 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 4 4 26 SUB_TILT NAME SUB_TILT PURPOSE Function to subtract tilt i e a straight line from profile data CATEGORY Topographic analysis CALLING SEQUENCE Result SUB_TILT X Y CURVATURE CURVATURE INPUTS X 1D array of lengths Y 1D array of heights KEYWORD PARAMETERS CURVATURE Set to subtract a 2nd order polynomial instead of a straight line OUTPUTS Result The new profile data EXAMPLE
72. uncher Programs File Screen Color Units Precision 2D Contour 3D Surface Height Histogram Radially Averaged PSD ER Plot Type Height Histogram ba Legend None j No Fill P J Condensed Colo y Title T Subtitle D X Min 0 00000000 Max 0 00000000 J Exact Log M Gid Tile H Y Min 0 00000000 Max 0 00000000 I Exact Log W Gid Tile m Done Refresh Rename Add Plot Delete Plot Files eflective rayOptics 33 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs File Screen Color Units Precision 2D Contour 3D Surface Height Histogram Radially Averaged PSD pa f EI S A Es D Le Al o 2 ai a Ke L E o a Q Plot Type PSD Radially Average y Legend None j No Fill P J Condensed Colo y PSD Fit Sigma x H sl Ft Label 5 jv a Title T Subtitle D X Min 0 00000000 Max 0 00000000 M Eat M log W Gid Tile D Y Min 0 00000000 Max 0 00000000 P Eat M Log W Gid gei M Done Refresh Rename Add Plot Delete Plot Files eflective rayOptics 34 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs TOPO Multiplot can also be u
73. ure 3 shows the TOPO Multiplot Files window after loading the same Nanoscope image we used in 3 3 Reflective rayOptics 28 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs IDL Read Command rd nanoscope xy z Read kel File jrenoscope sib el 20005 dat Only use surface data between 2 17 5614 ere 0 PSD Computation A Lb No Window AR bas Bed bez av kl Zero Padding I Only use PSD data between f 4 99021e and 0 0127750 144 Re Compute Figure 3 The TOPO Multiplot Files window after loading a surface data file Displayed below the File text box in the TOPO Multiplot Files window shown above is information regarding the contents of the file in this case the file contains a 512x512 image measured over an area 2 um x 2 um on Aug 19 2005 The next row of controls starting with the check box labeled Only use surface data between can be used to ignore surface data outside the Z range you specify For example if your AFM image includes a piece of dust you can limit the heights used to compute the PSD etc so that the dust is not included The next row down contains the controls used to determine how the PSD functions are computed See e g 4 4 28 The Radially Averaged PSD the X Averaged PSD and the Y Averaged PSD functions can each be displayed in a separate TOPO_psd window by clicking the corresponding Plot buttons that look like
74. used directly in your own IDL programs but you need to know their names in order to avoid inadvertent problems e g by using variables having the same names in your own IDL commands and programs In any case the TOPO routines uses a common block called TOPO defined as follows COMMON TOPO TOPO TOPO_HOME TOPO_BM The TOPO variable defined in the TOPO common block is an IDL structure variable and is the only common block variable that may be of use to you when writing your own IDL programs that use TOPO routines The TOPO variable structure tags that you can use are those that control the display of length and height variables and of length height and slope related parameters That is all surface data i e Y X and Z X Y must be defined in TOPO in units of angstroms However you can display surface data and surface derived quantities i e height and slope histograms and PSD and autocovariance functions along with fits to those functions in TOPO graphics routines using units of A nm um or mm Units can be controlled using the menu options in the TOPO Launcher programs described in the previous chapter Or displayed units can be controlled directly by setting the TOPO XUNITS_PTR and TOPO YUNITS_PTR structure tags at the command line or in your own IDL programs TOPO XUNITS_PTR An integer that defines the length units for displayed variables Set this variable to O for angstroms 1 for nm 2 for microns and 3 fo
75. ux system and you have installed topo in your home directory e g users joe topo Edittopo_cfg pro and replace the line if version os_family eq unix then topo_home dirt user_contrib topo with if version os_family eq unix then topo_home users joe topo 1 4 2 Other customizable settings There are other operating system and site specific settings that you can modify in the topo_cfg pro configuration file specifically those that control the fonts and special characters used by the TOPO graphical user interfaces GUI Please follow the instructions contained within the topo_cfg pro file to make such modifications If you are using TOPO on a unix platform you can also use the Xdefaults configuration file included in the topo extras directory to set some TOPO specific X windows preferences One method to do this is to copy the contents of topo extras Xdefaults into your personal Xdefaults file or into the IDL Xdefaults file dir resource X11 lib X11 app defaults Idl where dir is the IDL installation directory on your computer eflective rayOptics 12 7 October 2013 TOPO Version 2 2 TOPO Installation Guide 1 5 Common Installation Problems and Solutions Problem IDL can t find TOPO IDL gt run topo Error opening file File TOPO Solution You must add the TOPO installation directory to your IDL search path as described in 1 2 Problem The TOPO windows don t look rig
76. v_0x04100200 dat 5 1 9 V 3 DAT File Ji data _ nanoscope_example_4_v_0x04400003 dat 0 6 PN 532KB DAT File La media NAS1 M _ nanoscope_example_5_v_0x04100200 dat 8 1 005 V 520 KB DAT File B windt _ nanoscope_example_6_v_0x05120005 dat 8 AM lt B DAT File Downloads profile_data_example bd 9 2 M 18KB TXT File di Dropbox L PSD_r_example bd 01 V 9KB TXT File E Recent Places L PSD_x_example bd V 9KB TXT File WW Google Drive _ topomultiplot_example_1_measurement 013 10 V 757 KB TMP File Zi topomultiplot_example_1_measurement_ lv 3 Adobe Acrobat D HE Desktop 8 topomultiplot_example_1_measurement_ A Libraries E topomultiplot_example_1_measurement_ Documents 8 topomultiplot_example_1_measurement_ al Music FE tonomultinlot examnle 1 measurement File name nanoscope_example_6_v_0x05120005 dat ze The TOPO Surface Analysis window after opening this example file is shown in the next figure el TOPO Surface Analysis File Analysis Preferences Units Precision Help P V 36 04 A RMS 4 50 A 2 19960 86 20000 00 A 4 93 A I Subtract Polynomial 2 The Peak to Valley and RMS roughness values are displayed at the top left You can use the check box and text box at the bottom to subtract a polynomial from the image e g to remove piston tilt sphere etc offsets from the data As you move the mouse over the image the Z value is also displa
77. will be returned as a string array holding the comment lines included in the file GROUP GROUP_LEADER keyword passed to DIALOG _PICKFILE if FILE is not specified CANCEL Set this keyword to a named variable that will be returned to indicate if the user pressed the CANCEL button when prompted for a file to read if the FILE keyword is not set OUTPUTS If the V keyword is not used then the user must specify the correct number of Vi VO V1 etc output parameters There must be as many Vi s specified in the call to EROM as there are columns of data The V s are double precision arrays unless either the TAB or SEPARATOR keyword is specified in which case they are all string arrays RESTRICTIONS If EROM is called with the V keyword then the columns of data contained in the file are returned as double precision fields in the returned V structure variable Use of the V keyword requires that the data file contain at least one comment line and the last comment line MUST include the names of the data variables separated by the character For example to read a file using the V keyword containing three columns of 10 rows of data then the last comment line in the file must look like this First Variable Name Second One Another Variable Name Thus the V structure returned by EROM will have the following tag names HELP STR V V 0 VALUE DOUBLE Array 10 V O NAME STRING First Variable Name V 1 VALUE DOU
78. wo columns of data F and S then you can use the EROM routine as in eflective rayOptics 46 TOPO User s Manual 4 TOPO for IDL Programmers 7 October 2013 TOPO Version 2 2 EROM F S FILE MyProfile dat If your data is not in this form then you will probably need to write your own IDL procedure to read in the data with F and S as explicit parameters i e MY_PROCEDURE F S or Result MY_FUNCTION F Si Once the profile data are defined this routine uses the PLOT_PSD routine to display the results along with an optional fit 4 3 3 TOPO_surf NAME TOPO_SURF PURPOSE CAT A widget application for 2D surface analysis TEGORY Topographic analysis CALLING SEQUENCE OP TOPO_SURF X Y 2Z TIONAL INPUTS X 1D array of equally spaced lengths along X direction in angstroms Y 1D array of equally spaced lengths along Y direction in angstroms Z 2D array of heights in angstroms COMMON BLOCKS COMMON TOPO COMMON PLOT_PRINT RESTRICTIONS The X and Y values must be equally spaced X Y and Z must be in angstroms PROCEDURE Although X Y and Z must be in angstroms the units for displayed variables are determined by the values of the relevant tags of the common block variable TOPO That is set TOPO XUNITS_PTR to 0 for X and Y angstroms 1 for nm 2 for microns and 3 for mm Similarly set TOPO YUNITS_PTR to 0 for Z in angstroms 1 for nm 2 for microns and 3
79. y of height values the i th element of HIST is the density of heights in the i th bin of HEIGHTS NOLABEL Set to inhibit labeling the SIGMA and L values LABEL_ POSITION Integer specifying label position as per PLOT_TEXT eflective rayOptics 58 7 October 2013 TOPO Version 2 2 Plus most IDL PLOT graphics keywords RESTRICTIONS The units for X and Y must correspond to the values of the relevant tags of the common block variable TOPO That is set TOPO XUNITS_PTR to 0 for X in angstroms 1 for nm 2 for microns and 3 for mm Similarly set TOPO YUNITS_PTR to 0 for Y in angstroms 1 for nm 2 for microns and 3 for mm The precision of the fit parameters that are labeled on the plot is determined by the values of the variables TOPO XPRECISION for length related parameters e g correlation length and TOPO YPRECISION for height related parameters e g rms roughness For example if TOPO XPRECISION 3 then three places to the right of the decimal will be displayed PROCEDURE HEIGHT_DIST is used to compute the height histogram function MODIFICATION HISTORY David L Windt Bell Laboratories May 1997 4 4 11 PLOT_PROF NAME PLOT_PROF PURPOSE Procedure to plot a profile function CATEGORY Topographic analysis CALLING SEQUENCE PLOT_PROF X Y INPUTS X 1D array of lengths in units corresponding to the value of TOPO XUNITS_PTR Y 1D array of heights in units corresponding to the value
80. yed at the eflective rayOptics 25 7 October 2013 TOPO Version 2 2 TOPO User s Manual 3 TOPO Launcher Programs top and X and Y profiles are plotted in the windows below and to the left of the image respectively You can left click to capture an X profile row and right click to capture a Y profile column Here s how the window appears after we ve captured two X profiles and one Y profile we ve also adjusted the color table using the Preferences gt Adjust Color Table menu option Sl TOPO Surface Analysis File Analysis Preferences Units Precision Help H P v 36 04 A RMS 4 50 A Z 0 00 78 28 A 4 25 PROFILE Analyze Profile Export Profile Export PSD Remove Profile Remove All Profiles I Subtract Polynomial d Captured profiles are shown in the list located in the middle of the window and the corresponding surface profile and 1D PSD s are displayed in the plots on the right If a profile in the list is selected the 2 profile in the list is selected in the above figure you can click the Analyze Profile button to display the selected profile in a new TOPO_prof window You can also export to plain text files the selected 1D profile data and the corresponding 1D PSD data using the buttons labeled Export Profile and Export PSD respectively You can also export the profile data sent to TOPO prof using that program s File gt Export Profile
81. zip command Sgunzip topo_xxx tar gz followed by the tar command Star xvf topo_xxx tar Move the topo installation directory to the extensions directory in the XOP installation directory e g to xop2 3 extensions topo For Windows only e copy the file C xop2 3 extensions topo extras topo4xop bat to C xop2 3 topo4xop bat and e copythe file C xop2 3 extensions topo extras topo4xop vbs toC xop2 3 topo4xop vbs The name of the XOP installation directory depends on the version of XOP that you have installed and on where you have installed it on your computer For this step we ve assumed that XOP V2 3 is installed in the default location C xop2 3 However if you have a different version of XOP or a different installation location please substitute the correct name and path for your XOP installation directory above Note if you don t use the default installation location C xop2 3 you MUST edit topo4xop bat and specify the correct path to xop bat You might also want to make a shortcut on your Desktop to one or both of these files so you can start TOPO by double clicking that shortcut Use topo4xop vbs if it works on your system otherwise use topop4xop bat Start TOPO e For Windows Double click on topo4xop vbs or topo4xop bat if necessary Or start XOP and then use the XOP gt Load extension menu option to select topo4xop e For Linux Mac OS X Solaris At the command line type xop topo4xop eflective

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