LaDiCaoz and LiDARimager–MATLAB GUIs for LiDAR data
Contents
1. Set 4 to 3 and 5 to None and press button 1 Select fields 10 to 12 and press 14 to plot all views hillshade elevation slope and aspect image Investigate respective images to see how respective geomorphic features are expressed in different view options Enter output file name in field 16 e g Samplela select jpeg option in 17 and press button 18 Only images of currently open figures will be printed to file i e saved Enter output file name in field 16 e g Samplela select kmz option in 17 and press button 18 Only images of currently open figures will be printed to file i e saved Open respective kmz files in Google Earth to overlay hillshade plots etc with Google Earth imagery You may recognize the slight mismatch between kmz and base map imagery an issue we are currently working on Enter output file name in field 16 e g Samplel_ cut select asc option in 17 and press button 18 Before that zoom the hillshade map to an area similar to the one presented in Figure S3B Saving to asc will then create an ARC grid DEM with the spatial extent of the data presented in the hillshade view Change input file name in field 3 to the name used during step N in field 16 e g Samplel_cut set 4 to zero and press button 1 This will load the new and cropped DEM You may use this step if you have imported a large DEM using Quick draw and think to h2. 0 to the zenith 90 The lower the angle the darker the hillshade plot becomes Z factor allows increasing the contrast of the hillshade plot This may be helpful if the region or feature of interest has low relief e g fault trace offset channel You may invert the topography by using negative Z factors When the DEM was successfully loaded by pushing button 1 the minimum elevation value of the input DEM is plotted here During back slipping 41 this value 10 is adjusted to the minimum value that is displayed within the current zoom hillshade figure Figure S7 Also see explanation of field 12 When the DEM was successfully loaded by pushing button 1 the maximum elevation value of the input DEM is plotted here During back slipping 41 this value 11 is adjusted to the maximum value that is displayed within the current zoom hillshade figure Figure S7 Also see explanation of field 12 Figure S7 A Hillshade view of an example data set When using 13 to plot the DEM values 10 and 11 are set to be equal to maximum and minimum elevation within the imported data set all of A When using 41 to back slip the DEM currently presented in hillshade view the values in 10 and 11 are adjusted to display maximum and minimum elevation value within the current hillshade zoom e g in B This procedure is increasing computational efficiency Defines the number of contours plotted If you make a contour
3. accordingly Blue and red profile can be cut on both ends This is usually done with one profile e g the blue profile to improve calculation of the optimal offset the goal is to fit the channel profiles not the topography surrounding it Enter here the amount you want to cut off the start of the red profile Figure S9 Once you have entered a value the base map profile line and the Profiles figure will be updated accordingly Blue and red profile can be cut on both ends This is usually done with one profile e g the blue profile to improve calculation of the optimal offset the goal is to fit the channel profiles not the topography surrounding it Enter here the amount you want to cut off the end of the red profile Figure S9 Once you have entered a value the base map profile line and the Profiles figure will be updated accordingly Define the trend of the channel section cut by the blue profile Similar to button 14 pushing button 21 opens the base map figure Here you can enter start and end point of the channel trend line via mouse click After you entered both points a yellow dashed line is plotted in the base map plot outlining the channel trace The profile in the profiles figure will also be shifted accordingly accounting for channel obliquity relative to the fault trace Define the trend of the channel section cut by the red profile Similar to button 14 pushing button 22 opens the base map figure Here you c
4. again Enter output name used in step Y into field 3 e g Sample1 and press button 5 This will load all input data of a previously performed offset calculation and redraw the hillshade and profile figures Note that this step also adjusted parameters 7 to 9 After loading is complete close hillshade and profile figure again and press 13 This initialized the DEM with the new illumination parameters Now press 5 again All data required to perform the calculation are already entered You may press 39 to repeat the calculation and produce the GoF or change input parameters before you do so You can only back slip the topography after the GoF is calculated 20
5. in Figure S9 stretched by different z factors Qualitative comparison shows that using a stretch factor is to first order capable of accounting for variations in channel morphology evolution 14 32 Define minimum vertical shift of blue profile The tool was developed to match offset ephemeral stream channels Naturally the thalweg elevation at upstream and downstream profile location will be different otherwise channel gradient would be zero and no flow would occur To account for that and allow a better fit lower GoF of the channel profiles the GUI allows shifting the blue profile vertically When button 39 is pushed the blue profile is iteratively shifted in a vertical direction by a value between those entered in 32 and 34 using the increment size defined in field 33 33 Define vertical shift step size of blue profile See explanation for field 32 for further detail on the vertical shift 34 Define maximum vertical shift of blue profile See explanation for field 32 for further detail on the vertical shift 35 Define the minimum horizontal slip of the blue profile 36 Define the horizontal slip step size This value is not only the increment size precision in which the displacement will be measured It also defined the distance dx between profile points Figure S8 Once a new value is entered the red and blue profile in the profile figure is redrawn using the new step size 37 Define the maximum horizontal sli
6. may be imported to LaDiCaoz for exact measurement repetition and assessment Input data LaDiCaoz is using the same file format for input data as LiDARviewer We want to refer the reader to the corresponding section in the LiDARimagermanual LaDiCaoz GUI functionality To use LaDiCaoz start MATLAB and browse to the folder that contains both LaDiCaoz and the input data set Type LaDiCaoz in the command window press enter and the corresponding GUI appears Figure S6 presents a screen shot of the LaDiCaoz GUI Note that only one LaDiCaoz GUI may be open at any given time if an individual GUI such as LaDiCaoz is open more than once MATLAB will not know to which GUI individual inputs belong and an error messages occur Close all but one GUI to fix this problem In the following we will describe functionality of each button and editable field The order of descriptions from 1 to 49 approximately reflects the work flow when using LaDiCaoz 1 Push this button to load the input DEM An error message will appear if opening the file was not successful Check for typos in field 3 make sure the correct file extension 2 is chosen that the corresponding DEM is in the correct data format and that the DEM is in the same folder as the GUI 2s Select the DEM file you want to load Two types can be loaded asc ARC grid and asc ASCII grid where the prior refers to DEM saved in ESRI s ARCGIS ASCII grid while the latter refers to DEM
7. of original and back slipped topography Creation of these files requires re projection from UTM coordinates in which the imported DEM are stored to decimal degree geographic coordinates WGS84 and therefore definition of the UTM zone Enter the name used to store the saved data I recommend to use a unique name that refers to the individual offset i e back slipped feature One possibility is to include the distance to a reference point defined in field 42 in the name e g Ch6523 may refer to a Channel that is 65 23km away from the reference point If a channel has more than one downstream segment beheaded channels you may assign them letters ascending with offset amount e g Ch6523a is the smallest offset Ch6523b the next larger offset etc 16 49 Push this button to save the channel reconstruction Saving will create a number of files see Table S1 for explanation including parameter files images of current and back slipped topography and ASCII files of the along profile PDF and back slipped topography 50 This field allows entering comments regarding the offset geomorphic marker These comment will be plotted to the corresponding table in the html file File name Field Description 48 ext _Hshd jpg Hillshade plot of the topography presented in the current zoom of the hillshade plot window using the current illumination parameters 7 to 9 without fault profiles and channel orientation lines _Co
8. plot of the base map using 13 not of back slipped topography using 41 the elevation difference is equal to the maximum and minimum elevations within the imported data set respective values are presented in fields 11 and 10 so that you can determine the contour interval that corresponds to the contour number 11 10 12 contour interval If you make a 11 13 14 contour plot for back slipping 41 LaDiCaoz determines the maximum and minimum elevation value that is within the current zoom of the hillshade plot Figure S7 updates fields 10 and 11 accordingly and then uses 12 to determine the contour interval This procedure decreases computation time and focuses on the offset feature The contour interval is displayed in the MATLAB command window Push this button to plot the DEM using the afore specified options 6 and 10 12 Push this button to define the fault trend When button 14 is pushed LaDiCaoz opens the base map plot and allows to define start and end point of the fault trace via mouse click Move the mouse to one end of the fault trace and left click Then move to the other end of the fault trace and left click again We usually put a ruler onto the computer screen along the fault trace when tracing the fault After tracing after the 2 mouse click fault and profile line as well as the corresponding cross sectional profiles are drawn in hillshade plot and profiles plot respectively fault in turquoi
9. saved in a generic ASCII grid format see Input Data section and Figure S1 for further explanation on file format and conversion tools 3 Enter the file name of the DEM that is to be imported without its file extension 4 You may use a box car moving average to filter out holes and some high frequency noise signal in the DEM by entering the number of grid points over which the average elevation is to be calculated If you choose 0 grid points no average is used for 3 the average elevation of a 3x3 wide box around each grid point is determined and assigned to the center grid point This step will be performed during data import after pushing button 1 Note that averaging noticeably increases the data import time a Push this button if you want to look at i e re run a previous offset reconstruction The GUI is searching the current folder for an XX XX_parameter mat file where XXXX refers to the file name entered in field 3 Successful loading will open the DEM which has to be imported independently before 1 and plot fault and profile positions as well as channel trends as they have been defined in the previous run TO Q asc ARC gria 2 J 1 Load DEM 1 Adjust blue profile Stretch factor range min increment max Vertical back slip m min increment max Horizontal back slip m min left lateral 38 increment max NaN 37 O Number of iterations Figure S6 Screen shot of LaD
10. 51042 648 296834 648 304081 648 2947 12 648 348658 648 317707 648 305005 648 291785 648 2727 13 648 277412 648 282564 648 288102 648 250662 648 230 14 648 235677 648 218963 648 190351 648 190754 648 170 15 648 197716 648 218495 648 161613 648 209011 648 187 16 648 150000 648 135062 648 119354 648 125993 648 134 417 GAR 17SRQ1 GAR 147AKGA KAR ARAAR GAR ABARAA RAR ARII 472159 648 462898 437937 398039 8 648 442978 648 417915 648 396006 648 375694 648 370 9643 430000 648 409178 648 347498 648 350462 648 3474 648 412297 648 397671 648 356118 648 340920 648 314 1648 391824 648 351042 648 296834 648 304081 648 2947 648 348658 648 317707 648 305005 648 291785 648 2727 3 648 277412 648 282564 648 288102 648 250662 648 230 648 235677 648 218963 648 190351 648 190754 648 170 5 648 197716 648 218495 648 161613 648 209011 648 187 6 648 150000 648 135062 648 119354 648 125993 648 134 TIRAR 17SRQ1 KAR 147AKRA FAR ARKRAQAR KAR ARARAA RAR ARII nrows rows Figure S1 Possible input data formats for LiDARimagerand LaDiCaoz The input values for north south east and west define the spatial extent of the data set in UTM coordinates xllcorner and yllcorner refer to Easting and Northing coordinates of lower left corner of data set SW most data point n cols and n rows respectively refer to the number of rows along Northing and columns along Easting of the gridded DEM NoDATA serves as
11. 5x5 moving average and press button 1 again to reinitialize the imported data set Note the increase in loading time Press button 13 to see effect of moving average Repeat step F and G to see effect of varying box car sizes Change 4 to value of 3 and press button 1 We will be using this data set then for the remainder of the example DEM using a 3x3 moving average box car filter Press button 14 to define the fault line Move mouse to either end of the fault trace left click then move to the other end of the trace and left click again Fault and profile location are drawn as well as corresponding cross sectional profiles If necessary select Fault trace in 28 to shift the fault trace laterally using 23 for shift direction and 24 for shift amount and or rotate it in clockwise direction 25 or counter clockwise direction 26 using number of degrees defined in field 27 Repeat step J until actual and mapped fault trace match sufficiently well depending on actual fault geometry a precise fit may not be possible 18 Adjust location of blue and red profile by changing respective distance normal to fault in field 15 and 16 Cut blue profile to the approximate extent of the channel cross section You may use the Data Cursor in profiles figure see toolbar top of figure to determine left and right end points of the channel cross section Enter left end in field 17 and the right end in field 18 For f
12. LaDiCaoz azimuth and zenith are defined as indicated angle from south in counter clockwise direction and angle from horizon respectively 16 Enter name of the output file s without file extension Depending on file and plot option that was chosen 6 10 12 17 different files will be created Except for the asc option in 17 saved files have descriptive section attached to the entered file name Hillshad for hillshade plot Elevation for elevation plot Slope for slope plot and Aspect for aspect plot 17 18 Select file type option for output file You may save output as jpeg kmz and asc file The prior two options generate output files with of the plotted DEM images 6 10 12 The third option is using the spatial extent of the current zoom of the hillshade plot to save a corresponding subsection of the DEM to a asc file with name defined in 16 We recommend using this data set cropping option to increase computational efficiency when using the output data set asc file in LaDiCaoz See explanation for field 5 and Figure S3 for additional information when saving to asc file Save output data set using name and file type defined in fields 16 and 17 A message dialog box appears after the selected files were successfully saved Only data that are currently active plotted will be saved to file See explanation for field 5 for additional information when saving to as
13. Supplementary material to LaDiCaoz and LiDARimager MATLAB GUIs for LiDAR data handling and lateral displacement measurement Olaf Zielke J Ramon Arrowsmith School of Earth and Space Exploration Arizona State University Tempe AZ 85287 USA To whom correspondence should be addressed E mail olaf zielke asu edu Table of contents LAA Rita per manual ensena naen n E N E EEEa 2 PUOSC rerepa sakudiasnacdyoriwbatndcdesaie nae ude EREEREER E ERRE EEEE EEES 2 TO GU dataene ERE EEPE E EEEE E EEEE TEE EERI EEE 2 LiDARimagerGU Minictonality sctccciipecnseosanceteseedianideecccanaalvet lt seadsanidescceedae 4 Worked example sss aera reacs ena eo aan EESE ENEE EE EEEE EEEE 7 LaDiCaoz mana o cccsisasssancineadeaeaassaenad can asadaxadyaxeniaorentsaianian ceakearsaiaanenieoresaaanins 9 AUTOR Cio sundae a aonsenaan sea noascn canes E dea E E E ne 9 TIE datane oee e E E te roan E E 9 LaDiCaoz GUI Minctionality ccoricxacciexanrarxancciacariaxaonsiransadineceertdenissiiecsetoenesaie 10 Worked SX AADC cei cy Path ne hin en ienenunthasnieveawlaunanueves akduatsGennanhoasruseatshiuasemeae 18 LiDARimagermanual Purpose Purpose of LiDARimageris to facilitate the visualization and identification of horizontally offset geomorphic features such as fluvial channels as they cross a fault zone It further serves a the quick generation of LiDAR based imagery in publication quality b the generation of kmz files of these images that may be upl
14. alization of surface slope and aspect html A website that contains feature name offset measurements offset location and comments It also binds in the six jpg figures mentioned above assuming they are located in the same folder as the html file kmz A kmz file of the offset location for Google Earth The file further includes a pop up window that presents a table containing offset coordinates offset amount and range quality rating as well as the following images Hshd jpg BackslipHshd jpg ProfLoc jpg and _ Prof jpg _Parameters mat Parameters that populate the fields of the LaDiCaoz GUL If the user wants to look at an earlier reconstruction this file can be loaded by pressing button 5 after the DEM has been initialized before using 1 17 _Prof txt Contains two lines the first containing the input of field 42 45 46 and 43 The second line contains the scaled GoF as presented in the profiles plot bottom This GoF is cropped by the offset values entered in fields 45 and 46 _ProfLines txt Is a4 column table all values are in meters the first column contains the distance along the profile see profile figure XX XX_Prof jpg distance in upper and middle plot the second column contains initial blue profile elevation the third column contains initial red profile elevation the fourth column contains shifted blue profile elevation for
15. an enter start and end point of the channel trend line via mouse click After you entered both points a yellow dashed line is plotted in the base map plot outlining the channel trace The profile in the profiles figure will also be shifted accordingly accounting for channel obliquity relative to the fault trace 13 23 The four buttons Up Down Left and Right allow you to shift the fault trace or channel orientation lines To do so select the line that is to be shifted in 28 enter an offset amount in 24 and then press the button for the corresponding direction Shifting the fault line will also move the position of red and blue profile by the same amount and direction Thus after shifting profiles are redrawn in hillshade plot and profiles plot 24 Enter the amount in meters by which you want to shift the line selected in 28 25 You may adjust the orientation trend of upstream and downstream channel segment or fault trace by rotating it either clockwise or counter clockwise Press 25 to rotate the line selected in 28 by the amount defined in 27 in clockwise direction Profiles are redrawn in hillshade plot and profiles plot when features are rotated 26 You may adjust the orientation trend of upstream and downstream channel segment or fault trace by rotating it either clockwise or counter clockwise Press 25 to rotate the line selected in 28 by the amount defined in 27 in counter clockwise d
16. ave identified an offset feature You may crop and save to the surrounding of this feature creating a asc grid file 16 18 and then load it again without using Quick draw to increase the spatial resolution Otherwise you may use the Sample1l_cut asc file for further processing and offset measurement in LaDiCaoz LaDiCaoz manual Purpose The MATLAB based Lateral Displacement Calculator LaDiCaoz GUI was developed to allow quick and easy to reproduce measurements of tectonically offset sub linear geomorphic features e g fluvial channels based on LiDAR generated DEM The user may import and visualize the DEM create hillshade and contour plots define fault trace cross sectional profile position and orientation of the displaced geomorphic feature Then LaDiCaoz performs an automated offset calculation using the afore defined input parameters who s results may be assessed sub quantitatively and qualitatively by back slipping cross sectional profiles and topography respectively To ensure that the results of these measurements are as transparent and repeatable as possible we designed LaDiCaoz to create multiple output files including a high resolution images of current and back slipped topography hillshade and contour plots b images of profile position cross sectional profile relief and GoF plot and C a parameter file that stores all relevant data to repeat reload a previously made measurement those parameter files
17. c file Worked Example A B Start LiDARimagerin MATLAB prompt and make sure that DEM data set is located in the same folder Enter file name in field 3 file extension in field 2 and load options Here we use a sample data set called Sample1 asc that is saved in ARC grid Leave option 4 and 5 untouched and press 1 to load the data Close message dialog after in informed of successfully loading the DEM Press button 14 A hillshade plot that uses the illumination parameters specified in 7 9 is plotted Close the plot Change 7 to 220 8 to 35 and leave 9 at 1 Then press button 14 again to create hillshade plot with new illumination parameters Repeat steps C and D with varying values for 7 9 until you have gained good understanding of topography fault trace and offset features Change 4 to value of 5 thus using 5x5 moving average and press button 1 again to reinitialize the imported data set Note the increase in loading time Press button 14 to see effect of moving average Repeat step F and G to see effect of varying box car sizes Set 4 to zero again and change 5 to 2 Quick which loads only every 2 row and column of the imported data set 3 Quick loads every third row and column and so forth Then press 1 again to reinitialize the data set Press button 14 to see the effect of Quick draw Repeat step H and I to see effect of varying the grid size resolution
18. ce to assign the rating in the main text of the corresponding manuscript Enter the optimal offset estimate This value and the values entered in field 45 and 46 will be stored in an output file that allows creation of the along fault surface slip distribution Furthermore pushing button 49 saves the results it saves the current input parameters of LaDiCaoz the channel profiles the original base map the base map with channel and fault trace and the back slipped topography The values used for these back slip plots are the ones entered in field 44 Enter the minimum offset estimate This value is used to define the offset range that is capable of reasonably well reconstruction the initial topography and may be used to crop the GoF curve Figure S11B bottom to generate offset probability density functions PDFs See explanation for 44 for further detail Enter the maximum offset estimate This value is used to define the offset range that is capable of reasonably well reconstruction the initial topography and may be used to crop the GoF curve Figure S11B bottom to generate offset probability density functions PDFs See explanation for 44 for further detail Define the UTM parameters zone and hemisphere of the imported data set These parameters are used to create a kmz file that shows the offset position and also provides a table containing offset location coordinates offset amount assigned quality rating as well as images
19. d hillshade plot of topography to visually assess channel reconstruction back slipped by 6 0m 15 40 41 42 43 44 45 46 47 48 Enter the value in meter by which the base map will be back slipped Push this button to back slip the base map in the direction defined in field 38 by the amount defined in field 40 Depending on the selection in fields 6 12 a hillshade plot or contour plot will be produced The back slipped i e reconstructed surface may then be inspected to visually assess the quality of the reconstruction If reconstruction is not satisfying it is likely that channel trace fault trace or profile position may have been chosen unfavorably Note the importance of having a general idea of what the initial topography and channel morphology might have looked like the user has to make a conscious decision on what is considered the pre earthquake topography in other words what part of the profile should be correlated We recommend using both hillshade and contour plots for this step LaDiCaoz was written to reconstruct the 1857 surface slip distribution To allow easy visualization of the along fault slip distribution you can enter in this field the along fault distance to a reference point For the 1857 rupture trace we used the intersection of Hwy 46 and SAF fault trace Enter the quality rating assigned to the channel reconstruction Because this is a subjective procedure we present guidan
20. der as the GUI on Select the file type of the DEM file you want to load Two types can be loaded asc ARC grid and asc ASCII grid where the prior refers to DEM saved in ESRI s ARCGIS ASCII grid while the latter refers to DEM saved in a generic ASCII grid format see Figure S1 for examples 3 Enter the file name of the DEM that is to be imported without its file extension 4 You may use a box car moving average to filter out holes and some high frequency noise signal in the DEM by entering the number of grid points over which the average elevation is to be calculated If you choose 0 grid points no averaging is used for 3 the average elevation of a 3x3 wide box around each grid point is determined and assigned to the center grid point This step will be performed during data import after pushing button 1 Note that averaging noticeably increases the data import time 5 Choose this option to load only every 2 to 5 line and row of the DEM that is to be imported This option allows processing large high resolution DEM When None is chosen the whole data set is imported Select a value other than None if data import using None was unsuccessful and if MATLAB indicated a lack of available memory When you use the Quick draw option a value other than None and save to asc then the GUI will re import the original DEM at full resolution and select the values within the spatial extent of t
21. dummy value to identify grid points for which no elevation data exist cell size is distance in meter between data points equidistant in both directions A potential source for freely available LiDAR data stored in this format may be found at www opentopography org Figure S2 This portal for high resolution topographic data and tools allows among other options the generation of custom DEM and the download of 0 5m grid size standardized DEM IDW return or minimum return presented in Ikm tiles The latter DEM tiles are provided as binary ARC grid files that can not directly be imported into LiDARimageror LaDiCaoz You have to use one of the aforementioned conversion tools or any comparable 2 software package that is capable of converting binary ARC to ASCII grids When possible we recommend generation of custom DEM During this process you may choose interpolation method product download format grid resolution and search radius Figure S2 These options may be of particular importance when investigating areas with dense vegetation cover requiring adjustment of grid resolution and interpolation method For further instructions on how to acquire a custom DEM from www opentopography org and how to set the respective options we want to refer the reader to the help section of this web portal gt OpenTopography Portal x YN fi r http www opentopography org OpenTopography 7t Hvhteotton Resources Community Sup
22. e option that was re imported into LiDARimager without quick view option to present full data set resolution LiDARimagerGUI functionality To use LiDARviewer start MATLAB and browse to the folder that contains both LiDARimagerand the input data set Type LiDARviewer in the command window press enter and the GUI opens Figure S4 presents a screen shot of the LiDARimagerGUL Note that only one LiDARimagerGUI may be open at each time if more than one GUI is open MATLAB will not know to which GUI individual inputs belong and an error messages occur Close all but one GUI to fix this problem In the following we will describe the functionality of each button and editable field The order of descriptions from 1 to 18 reflects the work flow when using LiDARviewer BY LidARviewer o About Moving average box car over 0 4 Jid points Quick draw None Input file name G asc ARC grid 2 1 Load DEM file 1 Zenith Z factor Elevatior 10 UTM zone 11 15 emisphere N is _2 Plot Dem 14 jpg 17 2 Save image 18 Figure S4 Screen shot of LiDARviewer Circled numbers refer to list of different input options l Push this button to load the input DEM An error message will appear if opening the file was not successful Check for typos in field 3 make sure the correct file extension 2 is chosen that the corresponding DEM is in the correct data format and that the DEM is in the same fol
23. he hillshade plot to save them to the output file If you have not used the Quick draw option value is None then the GUI will export the portion of the already initialized DEM that is within the spatial extent of the hillshade plot That means if you have used moving average while not using Quick draw then the exported DEM will be the averaged one 6 Select this option to plot a hillshade view of the imported DEM when pressing button 14 Hillshade plots may be adjusted by changing the illumination angle azimuth and zenith and illumination contrast z factor fields 7 9 T Azimuth defines the horizontal angle of illumination Figure S5 The angle is measured in degrees 0 360 from south and in counter clockwise direction For example illumination from south to north has an azimuth of zero Illumination from east to west has an azimuth of 90degrees illumination from north to south an azimuth of 180degrees Note that depending on the azimuth the topography may appear inverted typically for azimuths below 90 and above 270 8 Zenith defines the vertical angle of illumination Figure S5 measured in degrees 0 90 from the horizon 0 to the zenith 90 The lower the angle the darker the hillshade plot becomes 9 Z factor allows increasing the contrast of the hillshade plot This may be helpful if the region or feature of interest has low relief e g fault trace offset channel You may invert the topograph
24. iCaoz Circled numbers refer to list of different input options We thematically color coded frames surrounding individual buttons and editable fields to improve layout and usability 6 Three options to plot the DEM base map are available You can select Hillshade to produce a hillshade map of the topography using the Azimuth Zenith and Z factor defined in field 7 8 and 9 You can select Contour to produce a contour plot of 10 10 11 12 the topography using the number of contours defined in 12 The third option is to select both hillshade and contour In this case the hillshade map is overlain by a contour plot using the contour number defined in 12 Generally it is recommend using only hillshade plots as base maps and not contour plots Contour plots are recommended for evaluation of the channel reconstruction during back slipping Azimuth defines the horizontal angle of illumination Figure S5 The angle is measured in degrees 0 360 from south and in counter clockwise direction For example illumination from south to north has an azimuth of zero Illumination from east to west has an azimuth of 90degrees illumination from north to south an azimuth of 180degrees Note that depending on the azimuth the topography may appear inverted typically for azimuths below 90 and above 270 Zenith defines the vertical angle of illumination Figure S5 measured in degrees 0 90 from the horizon
25. ield 18 you have to subtract right end point of channel from profile extent to cut off the last Xm of the profile You may do the same for the red profile Follow procedure describe under M Define trend of upstream and downstream channel segment using buttons 21 and 22 Line A refers to the orientation line that intersects the blue profile Line B refers to the orientation line that intersects the red profile Press 21 to start with the blue profile channel segment and use the mouse to trace the channel orientation same approach as for tracing the fault line see step I Then press 22 to trace the red profile channel segment orientation Follow step J to correct position and orientation of the trace lines select either Line A or Line B instead of Fault trace to move the respective line To increase computational efficiency now define parameter space for offset calculation Begin with stretch factor of 0 7 in field 29 0 1 in field 30 and 1 3 in field 31 Depending on the results after offset calculation 39 these values may be adjusted Use Data Cursor tool again see step M to determine the thalweg elevation of upstream and downstream profile in profile figure Use the value plus certain range for fields 32 to 34 For example thalweg elevation difference is approximately 1 0m then use 0 0 in field 32 0 1 in field 33 and 2 0 in field 34 Follow the same approach as in R to determine ap
26. imagerfeatures a quick view to load only every 2 to 5 line and row of the imported data set allowing to process significantly larger data sets If used the imported DEM have a lower spatial resolution than the original data set This resolution however is usually sufficient to depict fault trace and offset geomorphic features Figure S3A When output data are saved as asc file in LiDARviewer the GUI will use the spatial extent of the hillshade window Figure S3A inset B to crop and save a smaller section of the DEM For that the GUI opens the original data set and only imports data points within the spatial extent of the aforementioned hillshade window and then saves them to a asc file Thus using quick view does not result in a loss of data resolution when saved to asc format Figure S3B We typically use LiDARimagerto visualize large tiles of LiDAR generated DEM and to identify fault trace and offset features We then crop and save smaller sections of this data set for each offset features that was identified within the imported DEM Figure S3 A Hillshade plot of LiDAR generated DEM using the quick view option during data import here 3 Quick was used that is only every 3 row and column of the original data set is imported Original grid size is 0 25m grid size in A is 0 75m Topographic features are sufficiently represented to identify offset features B Example for an extracted DEM using the asc sav
27. irection Profiles are redrawn in hillshade plot and profiles plot when features are rotated 27 Enter the amount in degrees by which you want to rotate the line selected in 28 28 Select the line fault trace or channel segment orientation that you wish to either rotate or laterally shift You may choose more than one line 29 Define the minimum vertical stretch factor The blue profile can be adjusted by stretching it vertically changing its z factor to account for different morphologic evolution of upstream and downstream channel segment For example a beheaded channel may degrade diffusively lowering the channel profile relief while the respective head water is still active Stretching one profile vertically is a simple way of approximating the initial channel morphology Figure 10 When button 39 is pushed the blue profile will be stretched iteratively between the values entered in 29 and 31 using an increment size of 30 30 Define the vertical stretch factor step size See explanation for field 29 for further detail on the stretch factor 31 Define the maximum vertical stretch factor See explanation for field 29 for further detail on the stretch factor to to t1 t2 t1 z 2 Z z 0 5 Figure S10 Left and center figure show the diffusive evolution from t0 to t2 of a simple channel profile shifted in center figure to make the thalweg locations match Right figure shows an actual profile blue profile
28. l profiles not the topography surrounding it Enter here the amount you want to cut off the start of the blue profile Figure S9 Once you have entered a value the base map profile line and the Profiles figure will be updated accordingly 12 35 14 22 N Blue profile w Red profile 619 5 T T T T T 619 F 618 5 F 4 618 1 1 1 1 1 50 0 50 100 150 200 250 Distance along profile m Elevation m 618 5 T N 0 50 100 150 200 250 Distance along profile m Elevation m 3 a T S Figure S9 A Hillshade plot of an offset channel with fault trace in turquoise profile lines in red and blue and channel trend of upstream and downstream channel segment in yellow B Projected to account for channel obliquity relative to the fault trace topographic profiles Both profiles have been cut on both ends Start point of the profile is indicated by a dot in the hillshade view and corresponds to the left side of the topographic profile 18 19 20 21 22 Blue and red profile can be cut on both ends This is usually done with one profile e g the blue profile to improve calculation of the optimal offset the goal is to fit the channel profiles not the topography surrounding it Enter here the amount you want to cut off the end of the blue profile Figure S9 Once you have entered a value the base map profile line and the Profiles figure will be updated
29. nt jpg Contour plot of the topography presented in the current zoom of the hillshade plot window using current values for elevation range and contour number 10 to 12 _ProfLoc jpg Hillshade plot of the topography presented in the current zoom of the hillshade plot window using the current illumination parameters 7 to 9 with fault profiles and channel orientation lines _Prof jpg Image of both initial profiles red and blue profile Also shown is the back slipped blue profile back slipped by optimal slip estimate plotted on top of initial red profile This helps to visually assess the reliability of the determined offset amount whether the fit is reasonably good At the bottom is a plot of Goodness of fit GoF as a function of horizontal displacement for the optimal vertical shift and stretch of the blue profile _BackslipHshd jpg Back slipped hillshade image back slipped by amount defined in field 44 of the base map using extent of current zoom of hillshade plot figure and illumination parameters defined in fields 7 to 9 _ BackslipCont jpg Back slipped contour image back slipped by amount defined in field 44 of the base map using extent of current zoom of hillshade plot figure and contour plot parameters defined in fields 10 to 12 _Backslip asc ARC grid of back slipped topography using offset amount defined in field 44 This file may for example be plotted in LiDARimageragain for visu
30. oaded to Google Earth and c cropping of large data sets to increase processing efficiency in LaDiCaoz a tool to determine offsets of horizontally displaced geomorphic markers see following section of the supplementary material While LiDARimagerwas developed for LiDAR data processing it may be used to work with essentially any other gridded DEM e g USGS DEM SRTM that is presented in the correct input format see following section A number of conversion tools are available for the possibly required transformation of the input data format including ESRI s ARCGIS and FWtools based on open source GDAL Input data LiDARimagerand LaDiCaoz can read gridded DEM data stored in ESRI s non binary ARC grid format or a generic ASCII grid format Figure S1 presents example layouts of these data formats The data are required to be stored in x y z coordinates UTM coordinates to be processed in LiDARimageror LaDiCaoz Bi hcols 925 ii north 3905406 680000 2 nrows 847 ARC grid format 2 south 3904559 680000 ASCll grid format 3 xllcorner 244026 600000 Beast 244951 600000 4 ylicorner 3904559 680000 4 west 244026 600000 5 cellsize 1 000000 5 rows 847 6 NODATA value 9999 ncols 6 cols 925 cols 7648 472159 648 462898 437937 398039 8 648 442978 648 417915 648 396006 648 375694 648 370 9 648 430000 648 409178 648 347498 648 350462 648 347 10 648 412297 648 397671 648 356118 648 340920 648 314 11 648 391824 648 3
31. optimal fit Worked example Main components of LaDiCaoz are the GUI Figure S6 and the hillshade figure profiles figure and back slip figure While working on a channel reconstruction you should not close any of those windows as it may cause error messages If however such an error message occurs close all windows except the GUI and repeat the reconstruction algorithm In rare cases you still might get error messages Then close and restart LaDiCaoz completely The errors are mainly due to accidentally closing either hillshade or profiles figure A B 1T zo pa Start LaDiCaoz in MATLAB prompt and make sure that DEM data set is located in the same folder Enter file name of input data set DEM in field 3 file extension in field 2 Here we use a sample data set called Sample1 asc that is saved in ARC grid Leave option 4 untouched and press 1 to load the data Close message dialog after in informed of successfully loading the DEM Press button 13 A hillshade plot that uses the illumination parameters specified in 7 9 is plotted Close this plot again Change 7 to 220 8 to 35 and leave 9 at 1 Then press button 13 again to create hillshade plot with new illumination parameters Repeat steps C and D with varying values for 7 9 until you have gained good understanding of topography fault trace and offset features and created a nice base map Change 4 to value of 5 thus using
32. our will be generated To increase computational efficiency we recommend to zoom to a closer view so that not every data point has to be offset but only the once presented in current zoom Make hillshade and contour plots of the back slip by changing 6 and pressing 41 again 19 AA BB CC Visually assess how well the offset amount is able to reconstruct surface An unsatisfying fit while the cross sectional fit is satisfying is most likely due to an unfavorable tracing of upstream and or downstream channel segment Then repeat step P for either Line A or Line B and the steps following U including it to recalculate the optimal offset and back slip the topography again If the topographic reconstruction becomes satisfactory continue with the next step Use values bracketing the optimal offset enter them in field 40 and press 41 to back slip the topography Find bracketing values that are capable of reasonably well reconstructing what is considered the initial topography This trial and error approach is used to define the offset range Enter appropriate values to fields 42 to 47 the output file name e g Sample1 48 and press 49 to save the reconstruction After all data are successfully saved a message dialog will inform you about it Close all windows and also the LaDiCaoz GUI Start LaDiCaoz again see and follow step A to H After the DEM is initialized again Plot it once and close it
33. p of the blue profile 38 Define back slip direction This direction should be the opposite direction of the actual fault slip direction In other words select left lateral back slip for a right lateral fault such as the San Andreas Fault and vice versa 39 Using this button starts calculation of the optimal horizontal offset The GUI is going through all possible combinations of vertical stretch vertical shift and horizontal displacement Figure S11B middle and calculates the summed elevation difference between both profiles From the resulting three dimensional data cube the minimum summed elevation difference i e maximum Goodness of Fit GoF inverse of summed elevation difference is selected The corresponding optimal horizontal displacement vertical stretch and vertical displacement are displayed in the MATLAB window 35 14 22 N 50 100 150 200 250 Distance along profile m 0 6 0m re min Imax 119 47 39 W 0 gt 10 15 119 47 39 W Displacement m Figure S11 A Fault profile and channel segment location and orientation B Top panel shows overlay of red profile and back slipped blue profile using parameter combination that resulted in max GoF see bottom of S11B Middle panel shows parameters changed in offset calculation Bottom panel shows GoF as function of horizontal displacement for parameter combination vertical shift and stretch that contained max GoF C Back slippe
34. port if Pd Quicklinks T r To Er aha Point Cloud Data and Custom DEMs Standard DEMs Google Earth Files Tutorials f OpenTopography Portal C fi z hitp opentopo sdscedu s Point Cloud Data Download o Download raw data Query result in compressed ASCI File DEM Generation via Local Binning Algorithms Interpolation Method Product Download Format Yuin T Arc Gna ux meaag uean Ziow Point Count Algorithm Parameters o Gna Resoluton Detault 1 meter Enter radius value a Detauit 1 meter or x2y2 Resoluton whichever is greater DEM Generation via Spline Interpolation Algorithm Figure S2 Screen shots of www opentopography org web portal for freely available LIDAR data and tools A Main page of the site presenting different download options including Point Cloud Data and Custom DEMs and Standard DEMs B Spatial extent of B4 LiDAR data set along the southern San Andreas Fault and San Jacinto Fault in yellow Zoom to region of interest and interactively select area for which data are to be downloaded C Options of custom DEM generation including interpolation method grid size and search radius Consult the help provided on this site for additional explanation of respective options The maximum DEM size that LiDARimagerand LaDiCaoz can process depends on availability of memory DEM with lt 10 grid points work well in both GUIs for computers with gt 2Gb of memory LiDAR
35. proximate thalweg offset and add search range For example thalweg offset is approximately 6 0m then use 0 0 in field 35 0 1 in field 36 and 12 0 in field 37 Change field 36 from 0 1 to 2 0 This will not only decrease the increment number for offset calculation but also decrease the cross sectional profile resolution For simplicity both values are set to be equal Thus changing 36 is causing both profiles to be redrawn using the new resolution Set the value to 0 1 again Press 39 to start offset calculation This may take some time depending on defined parameter space in fields 29 to 37 After calculation is performed GoF and back slipped profile are presented Assess quality of offset estimate by studying the overlay of red and blue profile in top plot of profiles figure Optimal vertical stretch vertical displacement and horizontal displacement are presented in the MATLAB command window If cross sectional fit overlay of both profiles is good back slip topography by value with highest GoF to also evaluate topographic back slip If fit is not good you may have to adjust the parameter range in field 29 to 37 or change profile extent using fields 17 to 20 and repeat step U Enter optimal horizontal slip into field 40 and press 41 Remember that only the area of the current zoom of the hillshade figure is used for back slipping Depending on selection of field 6 a different back slip plot hillshade or cont
36. se profiles in red and blue The starting position of the profile left end in profiles plot is indicated by a dot in the base map Ensure that the fault trace is sufficiently long so that upstream and downstream cross sectional profiles are covering the offset geomorphic feature Also ensure that the traced fault is at the proper position and has the proper orientation You may use field 23 to 28 to adjust fault trace position and orientation accordingly The number of profile points is defined by profile length and the increment size in field 36 Each profile point is assigned the elevation of the nearest grid point Figure S8 Figure S8 Fault turquoise as well as red and blue profile lines across offset channel Profiles are parallel to the fault trace db and dr entered in fields 15 and 16 define the normal distance between fault trace line and respective profile Field 36 allows defining the increment size dx along the profile line The elevation of each profile point is set equal to the elevation of it nearest N neighbor grid point indicated by triangles in inset image 119 47 18 W Enter the distance between fault trace and blue profile line Figure S8 Enter the distance between fault trace and red profile line Figure S8 Blue and red profile can be cut on both ends This is usually done with one profile e g the blue profile to improve calculation of the optimal offset the goal is to fit the channe
37. y by using negative Z factors 10 Select this option to plot the elevation of the imported DEM when pressing button 14 11 Select this option to plot the slope of the imported DEM when pressing button 14 Slope refers to the steepness gradient of the surface at each grid point It is comparable to the Zenith of the illumination angle 12 Select this option to plot the aspect of the imported DEM when pressing button 14 Aspect refers to the dip direction of the surface at each grid point It is comparable to the Azimuth of the illumination angle 13 This option allows you to display a reference grid on top of the afore plotted visualizations of the DEM 6 and 10 12 when pressing button 14 14 Push this button to plot the DEM in the afore specified options 6 and 10 12 15 Define the UTM parameters zone and hemisphere of the imported data set These parameters are used when the kmz option in 17 is chosen which allows to create Google Earth kmz files Creation of these files requires re projection from UTM coordinates in which the imported DEM are stored to decimal degree geographic coordinates WGS84 and therefore definition of the UTM zone A z0 fB 35 14 20 N 35 14 20 N azimuth 119 47 37 W eee 119 47 37 W Figure S5 A and B Hillshade view of the topography at Bidart Fan in the Carrizo Plain San Andreas Fault exemplifying the effect of different illumination angles C in LiDARimagerand
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