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User`s Guide to COSI-CORR Co-registration of Optically Sensed

1. Window Size Size in pixels of the patches that will be correlated in X an Y direction Step This parameter determines the step in the X and Y direction in pixels between two sliding windows If the step is greater or equal to the window size then all measurements will be totally independent Search Range maximum distance in the X and Y direction in pixels where the displacements to measure are to be searched Grided Output Check this option if you want to obtain a displacement map with the top left corner coordinates to be integer multiple of the ground resolution This is mostly useful when several correlation of the same area need to be overlaid or mosaiced If unckeck the top left corner coordinates of the displacement map will be identical to the top left corner coordinates of the master image 28 10 3 Batch Correlation In situation where a lot of correlations have to be processed the manual selection of the correlation param eters through the COSI Corr GUI can be tedious Batching all the correlations using text files for the input parameters is possible Basically the user will feed 4 text files ascii format containing the list of master slave correlation parameters and output correlation file names to the batch correlation function Note that the correlation parameters and correlation filenames files are optional see below The execution of the batch can be operated through the COSI Corr GUI or
2. e Stack size Select the box width in pixel This size represents the number of pixel that will be average for each measurement along the profile e Image band Select the band s for which you would like to extract profile from e Display stack in ROI Check if you want a ROI representing the extent of the stacking box to be created Fig 25 top right panel You can manually delete these ROIs using the ROI tool afterward without affecting your stacked profiles e Plot Min Max stack if checked the minimum and maximum values for each value of the stack will be displayed on the profile window e Get profile click to get the stacked profile Fig 25 bottom left panel 11 9 Epipolar Projection This function Tools Epipolar Projection projects a displacement maps a correlation file which expresses the surface deformation in terms of East West and North South displacement components into a projection that expresses the displacement in Epipolar and Perpendicular Epipolar components This function is mostly useful when the topography residual is strong due to a poorly resolved DEM In theory all displacements due to uncorrected topography will be projected in the epipolar direction leaving the epipolar perpendicular projection free of topographic residual If the surface displacement is not entirely in the epipolar direction which would be unlucky the perpendicular epipolar component will contains
3. 11 1 Non Local Means Filter This tool Tools Non Local Means Filter is an implementation of the Non Local Means algorithm for denoising datasets and images This algorithm Buades et al 2008 and its derivatives Buades et al 2006 Goossens et al 2008 Zimmer et al 2008 have demonstrated an exceptional ability to preserve fine detail while reducing additive white Gaussian noise The most common application of the non local means algorithm is to the restoration of digital images The implementation provided here extends the method to denoising of scientific data sets in general A number of modifications to the original filter have been introduced in the literature We have chosen to implement modifications proposed in Buades et al 2006 Goossens et al 2008 Major features of our implementation include e Highly optimized native code that transparently and automatically exploits parallelism and media extension instructions for rapid processing of data sets SIMD instruction set 30 e Optional use of signal to noise weighting metrics for enhanced denoising e Ability to account for the presence of missing values NaN present within the input data set 11 1 1 Filter Process The non local means algorithm filters data by stepping through the data set one value at a time At each data point a small region of surrounding values typically 5x5 or 7x7 is compared with other non local regions patches of the same size
4. Ystart 1 File Type Envi standard Byte Order Host Intel 4AS May depends on your OS hardware Data Type Byte Interleave BSQ Once entered ENVI will create a hdr recording all these informations At that point the image is ready to be processed in ENVI and COSI Corr The first step is to create a COSI Corr ancillary file for the image This is done from the COSI Corr onglet in ENVI Cosi Corr gt Satellite Imagery gt Ancillary File Mars HiRISE or CTX and select the keyword lis that has been generated in the steps above From there you can follow the processing of earth based imagery as described in this user guide 6 3 Notes on HiRISE CTX specifics 7 If you are using HiRISE DTM and HiRISE orthos obtained from the HiRISE website both datasets need to be opened in ENVI using File Open External File MRO gt HiRISE RDR This is critical for the map projection information to be read properly Do not use File Open Image File on IMG or JP2 from HiRISE website HiRISE orthos are in JP2 format with an associated LBL file The LBL file found along the JP2 on the HiRISE website contains the map projection information of the image It is mandatory and must be stored in the same directory than the JP2 file HiRISE DTM map projection information is contained in IMG format and doesn t have a LBL file HiRISE DTMs downloaded from the HiRISE website need to be cleaned from missing values DTM border pixels are
5. 27 ns Previous Open y Figure 14 Spectral and Spatial selection tool for image detrending i teu eo DIANA O ss Ea File corr_hirise File corr_hirise Dims 1306 x 2752 Floating Point Dims 1306 x 2752 Foating Point Select Region From Image Subset ROI EVF Select Region From Image Subset ROI EVF Samples To 1306 NS 1306 ROI EVF oints Lines 1 To 2752 NL 2752 Full Size 14 376 448 bytes Subset Size 14 376 448 bytes Subset Using Image Map File ROWEVE Scroll Subset by mage Bay Ses Fevau open Figure 15 Spatial subset and ROI selection tool for image detrending 1 Select the bands to detrend This is done by using the Spectral Subset button of the ENVI File selection tool Fig 14 Default is to detrend all the bands 2 Select the spatial subset used to compute and apply the detrending Fig 15 left This is done using the Spatial Subset button of the ENVI File selection tool Fig 14 Default is to compute the polynomial fit and apply it to the full image extent 3 It is possible to define the area used for computing the polynomial fit through a ROI selection The ROT is selected in the Spatial Subset GUI Fig 15 left by clicking on the ROI EVF radio button and selecting the ROI of interest Fig 15 right For instance Figu
6. 45 no 6 pp 1529 1558 2007 and in F Ayoub S Leprince and J P Avouac Co registration and Correlation of Aerial Photographs for Ground Deformation Measurements Submitted 2007 Source Code is defined as code written in human readable format or in a high level program language a S c Derivative Works means any work consisting of revisions annotations elaborations or other modifications to Software which as a whole represent an original work of authorship Derivative Works includes any updates and new releases of the Software developed during the term of this license inclusive of backups updates or merged copies permitted hereunder including the file structures programming instructions user interfaces and screen formats and sequences 2 CIT retains ownership of any copyright rights to the Software licensed under this Agreement 3 CIT agrees to grant LICENSEE a nonexclusive non transferable royalty free license under the copy right rights and any applicable patent rights to use COSI Corr for internal research purposes only This license specifically excludes the right to sublicense COSI Corr in any form and it also excludes the right to use COSI Corr for any commercial or for profit purpose 4 LICENSEE agrees to grant Caltech a fully paid up royalty free nonexclusive license for educational and research purposes to any Derivative Works of Software that are owned or controlled by Licensee 5 LICENSEE may in
7. 47 6354779 b2 0 0397662 Affine transformation coefficients from Image to Camera X al al a2 y Y b0 b1 b2 y al 121 1030806 a1 0 0000175 a2 0 0209927 b0 124 8504385 b1 0 0209991 b2 0 0000126 Lense Radial Radial Measures KO 74567D 005 K1 30855D 009 K2 56084D 013 Lense Tangential Tangential Measures Po 0 D P1 O D P2 0 D Atmospheric Correction Output Select Interior Orientation File Not Selected Figure 3 Interior Orientation tool 4 Radial lenses distortions correction coefficients Depending on the data supplied by the calibration report enter directly the coefficients or compute them from laboratory measurements using the Radial Measures button 5 Tangential lenses distortions correction coefficients Currently only the coefficients can be entered if supplied by the calibration report The correction applied is the one described in Wolf amp Dewitt 2000 6 Atmospheric correction Check if you want to correct for atmospheric diffraction The correction assumes a standard atmosphere and follows the adapted method described in Wolf amp Dewitt 2000 Once the parameters are entered select a name for the IO file to be created and click OK Note 1 The radial and tangential lenses distortions as well as the atmospheric diffraction have typically an amplitude of around 1 to 4 jum only Due to the scanners resolution and stability consequences will not be dram
8. A larger region around the central patch is used as the search area The filtered value is computed as an average of the values within the search area weighted by their measure of similarity with the patch centered at the pixel to be filtered This approach has the effect of preserving true signals and features 31 Non Local Means Filter Select Bands to filter C Documents and SettingsNCosi Corr amp S TER Select SNR file optional Not Selected Band List Filter Params Advanced East West North South H noise parameter Search area dimension 21 Patch size 5x5 y Weighting method Averaging Linear regression Remove Band Restore all defaults Clear Band List Output Select Filtered bands file Not Selected Figure 12 Non Local Means Filter 1 Bands to filter Load one or more bands to be filtered Fig 12 2 SNR file optional A band weighting signal to noise ratio can be selected and applied during filtering The SNR file must have the same spatial size as the bands to be filtered should be floating point values comprised between 0 0 and 1 0 and will be applied to all bands selected 3 Upon loading the bands have been automatically assigned default filter parameters see 11 1 2 11 1 3 for parameters details Each band is associated with its own set of filter parameters and can therefore be processed with a set of data specific parameters if the user wishes C
9. November 2009 N Van Puymbroeck R Michel R Binet J P Avouac and J Taboury Measuring earthquakes from optical satellite images Applied Optics vol 39 no 20 pp 3486 to 3494 2000 P R Wolf and B A Dewitt Elements of Photogrammetry with Applications in GIS 3rd ed Mc Graw Hill 2000 A Buades B Coll and J M Morel NonLocal Image and Movie Denoising International Journal of Computer Vision vol 76 no 2 pp 123 to 139 2008 A Buades B Coll and J M Morel The staircasing effect in neighborhood filters and its solution IEEE transactions on Image Processing vol 15 no 6 pp 1499 to 1505 2006 B Goossens H Luong A Pizurica and W Philips An Improved Non Local Denoising Algorithm Pro ceedings of the 2008 International Workshop on Local and Non Local Approximation in Image Processing Lausanne Switzerland 2008 S Zimmer S Didas and J Weickert A Rotationally Invariant Block Matching Strategy Improving Image Denoising With Non Local Means Proceedings of the 2008 International Workshop on Local and Non Local Approximation in Image Processing Lausanne Switzerland 2008 49
10. for Linux Users johnMcClane Documents mySoftware cosi corr for Mac We ll refer to this cosi corr directory full path as pathToCosi for notation simplicity Each time you see pathToCosi you ll need to replace it by the full path The cosi corr directory contains the following fold ers save_add cosi modules and usgs The folder usgs contains the routines to pre process Mars imagery HiRISE and CTX If you do not plan to work on Mars imagery the usgs folder can be deleted Note that the routines use USGS ISIS software which is only available on Linux and Mac Follow the 4 steps decribed above to complete the installation 1 Copy the ENVI files envi cfg and e_locate pro in pathToCosi These files are found in the ENVI distribution usually in for example C Program Files ITT IDL71 products envi47 menu for Windows usr local exelis envi50 classic menu for Linux Applications exelis id182 for Mac Edit using a text editor the envi cfg that you copied in pathToCosi and specify the following e default save add directory pathTi oCosi save add e total cache size Mb 1000 e image tile size Mb 100 2 Create the two following environment variables IDL PATH and IDL_DLM_ PATH See below for OS specifics Don t forget here to enter the full path for instance home johnMcClane mySoftware cosi corr save add 3or more depending on your RAM available but don t allocate all of your RAM 4Not recommended to go o
11. 0 Installation eo c 4c 4 m dee Rx 24 Getting Help 24 0446 8646 m o Introduction A Typical Processing Chain Aerial Imagery Specific 4 1 Interior Orientation 4 2 Exterior Orientation Satellite Imagery Specific 5 1 Ancillary File ccoo consta 5 2 Satellite specifics o o Mars Imagery Specific 6 1 Ancillary File macs aa 6 2 HiRISE CTX general process pre COSI Corr 6 3 Notes on HiRISE CTX specifics Tie Points and GCPS 7 1 Tie points Selection T2 Tiep ints to GOPS eers a a g we ss GCPS Optimization 8 1 Miscellaneous seen Orthorectification and Resampling 9 1 Orthorectification les 10 Correlation and Displacement Measurements 10 1 Frequency Correlator 10 2 Statistical Correlator 10 3 Batch Correlation gt lt re ma saneras 10 3 1 Batch Correlation input parameters 10 3 2 Batch Correlation execution 11 Tools 11 1 Non Local Means Filter 11 1 1 Filter Process ss 2 o on s s 11 1 2 Filter Parameters Fig 12 11 1 3 Advanced Filter Parameters Fig 13 11 2 mago DIRE ias queo wg DR ARES SOS OSS Pee eee ox od 33 IL Image Warping ecaro n x X0 9 9 ox kg ko e SEE RR Roe RR ee 35 11 3 1 Image warping from Tie DOM S s lt seses oosa oko RR ORE 35 11 3 2 Image warping from correlation s a evs ma a GE O RR 36 11 4 Discard Replace Image Values
12. 41 Scroll 0 02203 MERA GRIEVE indicated principal point corner fiducials 0 000 mm 0 003 mm Indicated principal point midside fiducials 0 001 0 002 Principal point of autocollimation 0 0 0 0 Calibrated principal point point of symmetry 0 002 0 004 Fiducial Marks 103 9 6 mm 103 938 mm 103 944 103 941 103 938 103 954 103 929 103 938 113 002 0 013 0 008 112 990 112 993 OIA EUN 8 49 x 11 03 in 3 of 7 Figure 2 Fiducial points selection with the help of the calibration report The Aerial Imagery Interior Orientation Interior Orientation Setup function generates the Interior Orientation file and gathers the camera information read from the calibration report Fig 3 1 Calibrated focal length in meters 2 Principal point offset in millimeters 3 Fiducial measures You can enter the points either manually or by loading the file created with the Fiducial Points Selection Tool The 2D affine transformation between the image reference system and the camera reference system will be automatically computed 14 Si Interior Orientation EIE Camera Calibration No Camera Calibration o Input Cancel Focal Length meter 0 153715 _Load Principal Point x mm 0 002 y mm 0 004 Fiducial Points Fiducial Measures Affine transformation coefficients from Camera to Image al al x a2 y Y b0 b1 b2 y al 5942 0640865 a1 0 0284958 a2 47 6210981 b0 5773 7682321 b1
13. LOST PROFITS REGARDLESS OF WHETHER CIT SHALL BE ADVISED HAVE REASON TO KNOW OR IN FACT SHALL KNOW OF THE POSSIBILITY LICENSEE BEARS ALL RISK RELATING TO QUALITY AND PERFORMANCE OF SOFTWARE OR ANY DERIVATIVE WORKS THEREOF 11 All right title and interest in and to all data information and inventions that result from use of Software by the LICENSEE shall vest in and belong to the LICENSEE 12 This Agreement is governed by the laws of the State of California and any action brought hereunder shall be within the state of California 2 Installation and Getting Help 2 1 How to get COSI Corr Users must register through the Caltech Tectonics Observatory web site and accept the licensing agreement to download COSI Corr COSI Corr download A zipped package containing the COSI Corr module and the User s guide should be downloaded and installed Sec 2 2 2 3 All materials obtained are subject to the licensing agreement 2 2 Requirements COSI Corr has been mostly developed in IDL which is platform independent However for efficiency purposes some COSI Corr algorithms have been implemented in C C and fortran These compiled algorithms have been compiled and tested on Windows Linux and Mac OS systems but not extensively Requirements are e ENVI 4 7 and up www excelisvis com ENVI 5 users will need to use ENVI Classic which is bundled with ENVI 5 e 64b Windows Linux or Mac OS e At least 2Gb RAM e Multi cores proce
14. USGS script by doing command line ls norm cub gt normcube lis hi4socet pl normcube lis The first command will create an ascii file containing all the stripes names The second command will reconstruct an ideal full raw image The process is quite long few hours Once done the following files will be generated ESP 018039 1890 REDmos hijitreged norm noproj 8bit cub ESP 018039 1890 REDmos hijitreged norm noproj cub ESP 018039 1890 REDmos hijitreged keywords lis ESP 018039 1890 REDmos hijitreged raw ESP 018039 1890 STRETCH PAIRS lis flat f m1 txt flat f1m2 txt flat f2m3 txt flat f3m4 txt flat f4m5 txt flat fbm6 txt flat f6m7 txt flat 7m8 txt hi4socet prt hinoproj prt The files in red are the files needed to move to COSI Corr raw is the raw binary reconstructed image and keyword lis is a text file containing the ancillary information of the image 3 Before opening the raw in ENVI you need to retrieve the number of lines and columns of the image This information can be found in the keyword lis keywords TOTAL LINES TOTAL SAMPLES 8http isis astrogeology usgs gov IsisWorkshop index php Working with Mars Reconnaissance Orbiter HiRISE Data 18 When opening for the first time the raw in ENVI you will be asked to enter the header information of the image Samples number of columns TOTAL_SAMPLES Lines number of lines TOTAL_LINES Bands 1 Offset 0 Xstart 1
15. band projection i e in the E W and N S projection for a regular correlation file Profiles can also be projected in the fault parallel and fault normal directions using Options Profiles Projection It is assumed for the Parallel Normal projection to receive a two or more bands file with first and second bands representing the E W and N S displacements a correlation file typically For each stacked profile the fit range can be customized on the left and right part of the profile as well as on the available bands The range can be changed by moving the green rulers with the mouse or by entering range values in the appropriate fields Output A stack project can be saved restored using File Save Stack Restore Stack Note that only the stacks size positions and fit ranges will be saved You will be asked to enter the image and fault file when restoring When done with adjusting the profiles two options are available to export them e File Export gt Fault Displacement will save the fault offset measure location geographic coordi nates its values E W N S or Parallel Normal depending on the chosen projection and the sigmas e File Export gt Full Stack Information will save in addition the details of each stacks box size profiles stacked 44 The possibility of weighting the sigmas is offered before exporting the data For example if the measures in the correlation file are not totally indep
16. ee es 31 Non Local Means Filter Advanced Parameters 2 22222 llle 33 mago Detrendmm aia ee Pe od A AAA e d dede de Poe ege ES 34 Image Detrendig 22e e ok eh woo mao o Pop og Re Dy RR RR OY xd 34 Image Detrendmg ci e EE SG Ge A xp Ry E oce ee ud 35 LnaseDetrendig un s e Gora RON ee OG RUE ERN RERO woo 36 Image WSEDR E eca ssa ox Rok 350 9 be ROS RR RR a RR an e X AUR AA 37 lenge Filter WIBOOW 0 003 0003 aa d woo monem m a ER Re Pee ea ee e de 38 Destripping Selection Window 2222s 39 Destripping Stacking Window 0604446508 0600 4 a ee eS 41 Destrippine Cortectod Window 22 re e crsa daaa 02246446620 bb be RRR ea 42 Vector Pield WindoW 4 lt 6642 24445444 604 dog ed mee des dem EES 43 Profile Stacking Window sarira 2 42484 06 0020 a EE ee DSSS OEE EE SS 44 Mannal Stacking oca ee PERE Ree ES A ee Les eee EY d 45 Bpapolar Projection aaa oe EO ADR RRA ORE YE OEE E NOR A BURNS ey a 47 of Tables 1 Preface 1 1 About This Document Section 1 presents some general information about COSI Corr Section 2 presents the COSI Corr download ing instructions and installation guidelines Section 3 presents the successive steps necessary to process a pair of images Sections 4 to 10 detail each function available in COSI Corr their chronology reflects more or less the chronology presented in section 3 1 2 Who Will Use This Document This documentation is aimed at scientists whose interest is in working
17. es 38 1S Destr pe TAS a o C a ae Ee OD TTTT 38 11 51 Manual Orientation sR AA ws Bee wen dece MGS gg 39 11 5 2 Automatic Orientation gt o sss radiri kassasi eaan rrera 40 Wile Vector Fld a ico a RO QN 9 x6 on XR XS a AA GE OS E e 40 ILY Stack Pranles 2 n0 ea A a a FUR we ee ow v Uu 42 IL quent Balboa oe 3h34 ee dic GR BS a 42 DIG OS 4476909 AAA 43 118 Mannal Stacking Profiles o 05 93 9 goo OR OR XXX MEO doy o a P x d 45 119 Epipolar Projections 72224 nos gk ED eee S C9 Wo E ER A ow od 46 12 Miscellaneous 47 List aOANoa rwner M2 h2 h2 hO h2 h2 h2 n2 L2 L2 LS BRP ERR Ew O04 0r 00 05 1joc0U c0 tN o0 List of Figures COSEComn mto ENYD ss im Hebe eb eee exe RR aS poe Yo wv s 12 Aerial image fiducial points selection eh 14 Interior Orientation Window lt c o coco eaaa wesu naa Sap e a ed p 8 zur ys 15 Exterior Orientation Window gt 30 Rb RE ES ee 8o x ERG a a a ee G a 16 Tie Ponte to GUS Window lt i gt 546544 seb ebb ESE de ob Ros wok A a 20 GOPS text File Format 2 0 5 2 nen 4 how aaa eS EE EE A ee REE EEE 21 GOPS Optimisation Window 4 2 0 2 2 oS Sk SS eee o4 ee 9b 22 Orihoresampling Window sa oo wb UG Romx PE SWRA BORE Bm x 25 Correlation Window lt lt lt span fee ena wae E E E PUR oe de eGo ee a 26 Frequency Correlator Window o cc c c to o oe todi o oom eee ed eS 27 Statistic Correlator Window s 4 ee eR RA ee a RO 28 Non Lacal Means Filter 222 222 2 e woe REE ee ee ee
18. fequential correlator is advised when the reference image is an orthorectified image For more information on the correlator engines and their options see Sec 10 Weight GCP with correlation SNR If checked GCPS will be weighted with the correlation SNR of the previous loop This allows to give more weight on GCPS whose patches have a better correlation For the initialization GCPS will be assigned the SNR read from the GCPS file or assigned an equal SNR in case of tie points and ICP files If not checked GCPS will be constantly weighted with the SNR from the initialization 23 e Dynamic display of optimization If checked a graphic window displaying the successive patches will be displayed as the optimization goes This allows for a visual check of the patches that are correlated For instance it is a convenient way to check that GCPS have not been chosen too close to the images borders 7 Optimized GCPS Select the filename of the optimized GCPS that will be created The Select All button allows you to select successively all the files necessary Besides the optimized GCPS the output file will also contain a record of the files and parameters used as well as information on the optimization The average and standard deviation of the mis registrations in each North South and East West component are recorded at each iteration This allows to check the convergence of the process and the quality of
19. filled with the value 34e38 which will corrupt any subsequent processing These values need to be replaced with more plausible values e g average of the local topography etc To do that you can use the Cosi Corr Satellite Imagery Ancillary File gt Mars gt Clean DTM tool The average elevation of the scene will be computed and will replace missing values Alternatively you can replace the missing values by the value of your choice using Cosi Corr Tools gt Discard Replace Image Values In both cases do not forget to open the DTM to clean using File gt Open External File MRO HiRISE RDR for the map information to be forwarded to the cleaned DTM correctly Once the DTM is cleaned you can save it as a regular ENVI file Tie Points and GCPS 7 1 Tie points Selection The tie points selection consists of pairing similar points between two images It will most of the time consists in associating points between a georeferenced image and a non georeferenced image typically between an orthorectified image and a raw image It allows to associate a ground coordinates to a point in a raw image 1 Open the two images for the tie points selection 19 Select the Tie Points GCP Select Tie Points Image to Image tool Base Image refers to the georeferenced image master and Warp Image refers to the raw image slave Select tie points between images See ENVI Help for more details on this func
20. install the software binaries Second you install the data which contain all the imagery ancillary information Beware the data files are very large gt 50Gb for MRO mission only If you plan to use only HiRISE and or CTX you just need to download the MRO mission data e Edit and update USGS code hi4socet pl located in pathToCosi usgs to proper path In the early lines replace hinoproj path usgs cdev contrib bin to hinoproj_path path To Cosi usgs 4 Check COSI Corr installation a Launch ENVI For Windows user launch ENVI or ENVI Classic if you have ENVI 5 For Linux and Mac user start a new terminal and type envi if using ENVI 4 7 or 4 8 envi classic W if using ENVI 5 0 and above Mac users note that it is not recommended to use the Mac OS GUI to launch ENVI The COSI Corr menu should appear in the ENVI tool bar Fig 1 If it is not please check that you updated the envi cfg file correctly and that the IDL PATH is correct Once the COSI Corr menu is displayed in the ENVI toolbar do Cosi Corr About Cosi Corr Information about COSI Corr should appear If an error message is displayed instead please check theIDL DLM PATH and the LD_LIBRARY_PATH for Linux or DYLD LIBRARY PATH for Mac are correct gt e c m gt It is recommended to register and visit regularly the COSI Corr forum http www tectonics caltech edu forum where you will find tips bug reports thematic tec
21. remotely sensed images the correlation can be applied to any types of images Several post processing utilities are available such as denoising vector field display profile stacking tool and destriping tools COSI Corr has been designed to retrieve the sub pixel displacements between optical images However it is necessary to understand that even though images will be used to their full extent limiting factors such as uncorrected topography noise resolution will affect the measurement results 1 4 Support COSI Corr has been developed at the California Institute of Technology Caltech supported by the Caltech Tectonics Observatory the Moore Fundation and the Keck Institute for Space Studies 1 5 Citation The Caltech Tectonics Observatory TO is making this module available to you in hopes that the software will enhance your research A number of individuals have contributed to the development of COSI Corr The authors would like to thank R mi Michel and Renaud Binet for their insightful comments and their early work in the field of sub pixel image registration and correlation Van Puymbroeck et al 2000 We also thank Sylvain Barbot for his work on the SPOT 5 ancillary data and David Fanning for some IDL functions The COSI Corr development team asks that you cite S Leprince S Barbot F Ayoub and J P Avouac Automatic and Precise Ortho rectification Coregistration and Subpixel Correlation of Satellite Images Ap
22. the fault trace file will be considered the fault origin which will be the top pixel line wise of the fault trace 3 Oriented Fault File Select the oriented fault profile file name to be created 11 7 2 Stack This tool Tools Stacking Stack manages the stacking boxes and resulting profiles Fig 24 A stacking box is defined by its width and length which are expressed in pixels and must be odd The box is centered on a pixel belonging to the fault For each selected bands profiles in the box length direction are retrieved and stacked The resulting profile is displayed and the offset at the fault position can be measured using linear fit on the resulting profile Stacking Box Initialization Boxes can be initialized using Options Initialize Profile and or can be added or deleted one by one using the Add and Remove buttons There are two ways to initialize stacks e Stack number Select the number of stack to extract Stacks will be evenly spread along the fault profile e Stack spacing pix Select the spacing in pixel between stacks A spacing of 1 means that a stack will be extracted for every pixel of the fault profile minus edge effect at the extremities of the fault profile Use this initialization if you want a continuous fault slip measurement along the fault profile Size and center position of the selected box can be changed with Stack Length odd and Stack Wi
23. through the IDL ENVI command line as explained below 10 3 1 Batch Correlation input parameters The ascii formats of the text file are the following e Master file This file is mandatory One image per line and for each image line the number of elements can be either 1 2 or 6 l element filename full path The first band and full extent of the image will be correlated For instance home johnMclane studyCase master tif home johnMclane studyCase2 master tif home johnMclane studyCase3 master3 tif 2 elements filename full path band number first band 1 This allows to select the band to be correlated This is only useful for multiband image and when the band to correlate is not the first band Full extent of the image will be correlated For instance home johnMclane studyCase master tif 1 home johnMclane studyCase2 master tif 2 home johnMclane studyCase3 master3 tif 2 6 elements filename full path band number spatial extent Xstart Xend Ystart Yend This allows to select a subset of the master image to correlate The spatial extent is expressed in pixel top left pixel coordinates are 1 1 For instance home johnMclane studyCase master tif 1 500 2564 758 6225 home johnMclane studyCase2 master tif 2 1 500 1 700 A given master text file can use the three options 1 2 6 elements home johnMclane studyCase master tif 1 500 2564 758 6225 home johnMclane studyCase master tif home johnMclan
24. with optical remotely sensed images aerials or satellites Users are likely to be Earth scientists looking for seismic ground deformations glacier flows sand dune displacements slow landslides or more generally looking for horizontal changes between multi temporal images Users do not need to have a programming background but will need some familiarities with the concepts and vocabulary of remote sensing A basic knowledge of the ENVI software will be useful as COSI Corr is integrated in ENVI 1 3 About COSI Corr The COSI Corr software has been developed by Fran ois Ayoub S bastien Leprince and Jean Philippe Avouac PI and is mainly an implementation of the procedures described in e S Leprince S Barbot F Ayoub and J P Avouac Automatic and Precise Ortho rectification Coreg istration and Subpixel Correlation of Satellite Images Application to Ground Deformation Measure ments IEEE Transactions on Geoscience and Remote Sensing vol 45 no 6 pp 1529 1558 2007 Leprince et al 2007 e F Ayoub S Leprince and J P Avouac Co registration and Correlation of Aerial Photographs for Ground Deformation Measurements ISPRS Journal of Photogrammetry and Remote Sensing vol 64 no 6 pp 551 560 November 2009 Ayoub et al 2009 The main tasks performed by COSI Corr are precise orthorectification images co registration and cor relation Although the orthorectification and co registration are tailored for
25. 0000000 Minimum of weights 6 Y Center data point Omit Y Noise parameter Fixed Y Weighting type Bisquare Figure 13 Non Local Means Filter Advanced Parameters Center data point Indicates whether or not the center data point i e the data point being filtered is included in the weight calculation The default condition is to omit the center data point in the weighting calculation Noise parameter Indicates whether the noise parameter H is fixed at the user supplied value Otherwise an adaptive algorithm Zimmer et al 2008 is used to select the noise parameter at each filtering point This adaptive method works poorly and it is not advised to use it but it is left here for further tests and developments Weighting type Refers to the way the local weights relate to the patches similarity measurements Standard Computes the patch weights according to a Gaussian distribution Buades et al 2008 Bisquare A modified form of Standard with a finite taper and steeper fall off Goossens et al 2008 Modified Bisquare A modified form of Bisquare but with even steeper taper and fall off Goossens et al 2008 The Standard i e Gaussian and the Bisquare methods have proven to be the most useful in our tests Note that for a given noise level in an image a particular value of H has to be selected for each method NOTE The denoising results provided by the filter using the default p
26. 3 2 Image warping from correlation Refer to Figure 18 right panel 1 Slave Image to Warp Select the slave image to be warped according to the correlation between a master and the slave images The user can select the bands to warp default is to warp all bands and can select a spatial subset to warp 36 Input Slave image to wrap Not Selected Master image Not Selected Slave image to wrap Not Selected Select Conelation file Not Selected Select Tie points file Not Selected Options Output grid Poems Select output grid 9 Thin plate spline fit of the tie points Not Defined Polynomial fit of tie points omial fit degree 2 E Save wrapping matrice Not saved 3 Resampling Kemel 1 m y Dense wrapping fromthe conelation Polynomial ft degree 2 gt Output Polynomial fit from the correlation Resto Re B Memo Subset fit area through ROI ES 7 Save wrapping matrice Not saved Resampling Kemel Output Output Result to 9 File Memory Enter Output Filename Figure 18 Image warping from tie points left or correlation right 2 Correlation file Select the correlation file It is expected that the first band selected is the E W column displacement and the second band selected is the N S line displacement If the master or slave im
27. Master Image Select the master image onto which the slave image is going to be warped on Normally tie points are selected between this image and the slave image selected previously The master grid defines the grid of the warped slave The user can change the grid onto which the slave will be warped on using a spatial subset Tie points file Select the tie points file ascii format The format of the file should be one tie point per line with the format of a line X master Y master X slave Y slave Coordinates are in pixels A graphical tool to select the tie points between the master and slave image is available at COSI Corr gt Tie ponts GCPS Select Tie points Image to Image or at Map Registration Select GCPS Image to Image Select the warping function either a Thin plate spline needs at least 7 non colinear tie points or a polynomial surface fit The mapping matrice defined from the tie points and the function used can be saved if needed either on disk or in ENVI memory beware of potential large size of the mapping matrice Select the resampling kernel used to resample the slave image according to the mapping Options are described in Sec 9 1 Select the warped slave output type either on disk need to provide a file name or in ENVI memory Note that this function is very similar to ENVI function Map Warp from GCPS Image to Image with the added Thin plate spline fit and sinc resampler option 11
28. Save non detrended bands Check the box if you want the output file to contains bands that are not detrended i e simple copy of the non detrended bands of the image 11 3 Image Warping This tool allows you to warp an image slave to another image master according to a set of tie points between the master and slave image or according to a correlation map obtained between the master and slave Both methods are a 2 steps processes the first step defines the mapping of the warping according to the tie points or correlation map and the second step resamples the slave according to the mapping defined in the first step 11 3 1 Image warping from tie points Refer to Figure 18 left panel 1 Slave Image to Warp Select the slave image to be warped according to the tie points defined between the master and the slave The user can select the bands to warp default is to warp all bands and can select a spatial subset of the slave to warp In case of a spatial subset all the tie points present in the tie points file are used to define the warping even those outside the spatial subset but only the spatial subset is warped according to the mapping 35 7 Input Decimation step pix 10 Polynomial fit degree 2 y Fit iteration 2 Output E Save non detrended bands Output Result to File Memory Enter Output Filename Choose Figure 17 Detrending image parameters selection GUI
29. Seismo Angle to rotate image to stack stipes undulations vertically degree 180 1 Select Image to apply correction to if different Not Selected Output Select Corrected File leave empty for in memory Not Selected Figure 20 Destripping tool selection 11 5 1 Manual Orientation 1 Tmage to define correction from Select the bands usually only the EW and NS bands from which the correction will be defined Fig 20 Angle to rotate image The stripes stacking is operated vertically If the stripes are not vertical the image must be rotated to align vertically the stripes Enter the rotation angle degree necessary to align the stripes vertically Tip the ENVI rotate tool Basics Tools Rotate Flip Data can be used first to determine precisely the angle Image to apply the correction to if different If the corrections are meant to be applied to a file different than the one they are determined from select it accordingly It must be of the same size with the same number of bands that the file used to determine the correction A typical case is when a denoised and smoothed correlation file is used to determine the stripes correction but the correction is applied to the raw correlation file If this field is left empty the correction will be applied to the file from which the correction is determined Corrected File Select the filename to create if you want to save it to the d
30. Tools Vector Field displays a vector field based on displacement maps or ASCII files Loading Data To load data in the Vector Field tool do File Open Two kinds of data can be entered ENVI File When selected you will be prompted to enter the E W band and N S band successively of a displacement map to construct the vector field The E W and N S band selected and their subset must be of the same size and must be georeferenced A typical entry is a correlation file 40 B Select subset to stack vertically in rotated image E E Available Bands List Sel le Optio Select Input File File Information 2 E 1 Memory13 CorrelationSeismo Sl Select Spatial Subset File Memory13 Dims 694 x 721 Floating Point Samples il To 694 Ns 694 Lines 1 Tofa wu 721 Full Size 2 001 496 bytes Subset Size 2 001 496 bytes Subset by Image Map File C crol Subset by Image Input Band Reset Previous OK Cancel Samples 510 lt Lines 8s8 OK Canes Figure 21 Destripping tool stacking area definition e TXT File An ASCII file which must be of the form Easting Northing DEasting DNorthing DEasting and DNorthing refer to the vector value in Easting and Northing directions at the location indicated by Easting and Northing A typical entry is GPS measurements file Note that additional data from ENVI file or TXT file can be added to the vector field display but t
31. User s Guide to COSI CORR Co registration of Optically Sensed Images and Correlation Francois Ayoub S bastien Leprince and Jean Philippe Avouac California Institute of Technology 1200 East California Blvd Pasadena CA 91125 USA February 2 2015 Abstract This document is a user s guide for the installation and the use of COSI Corr COSI Corr is a software module integrated in ENVI which provides tools to accurately orthorectify co register and correlate optical remotely sensed images frame and pushbroom satellite images with the ultimate objective of retrieving ground surface deformation from multi temporal images Although this module is tailored to measure ground deformations such as coseismic deformation glacier flows sand dune migrations slow landslides etc it can also be a valuable tool for many other change detection applications requiring accurate coregistration of images A sub pixel detection capability is expected depending on the quality and the noise level of the data COSI Corr User s Manual February 2 2015 Copyright 2007 2014 California Institute of Technology Contents 1 Preface 1 1 About This Document 1 2 Who Will Use This Document L3 About COSLCof amp 9 99a LA SUpport soe woke y oy vb l5 CeO osas gg he wR kk 4 d Lo Declaro aa ow ee ee ee Installation and Getting Help 2 1 How to get COSI Corr 2 2 Requirements o 2
32. able package to be installed on your computer If it is not already installed from a previous software installation you can download the package here http www microsoft com en us download In Popular downloads select the Devel oper Tools category and download the Visual C Redistributable Packages for Visual Studio click on the blue link and follow instructions Reboot your computer Linux OS You need to update your startup shell script to indicate to the operating system where the necessary COSI Corr files are Most Linux distributions use the bash shell by default although several other shell are available bash csh zsh etc If you don t know which is your default shell you can find out by typing in a terminal the following ps p Examples on how to update you startup shell script are given for the bash shell If you are using a different shell please refer to its documentation to create environment variable Edit your bashrc file using a text editor The bashrc file is usually located in your home directory e g home johnMcClane Warning the bashrc is a hidden file so you may need to activate the show hidden files if you are using the GUI interface of Linux Edit the bashrc file and add the following at the end of the file source usr local exelis envi50 bin envi_setup bash export IDL PATH pathToCosi IDL DEFAULT export IDL DLM PATH pathToCosi cosi modules IDL DEFAULT export PATH PATH pathToC
33. ach band prior to running the filter The noise standard deviation can be estimated from the image local statistics observed over areas with presumably constant values The ENVI ROI tools can be conveniently used to this end Search area dimension This number refers to the dimensions of the search area around each data point Since the shape of the area is fixed as a square the user need only supply one value indicating the dimension of the side For example if the user enters 17 this instructs the application to use a search area of size 17 x 17 pixels The default value is 21 corresponding to a search area of 21 x 21 data points This value must be an integer smaller than the smallest data set dimension CAUTION Large search areas will cause the application to be unresponsive for long periods of time In general areas sizes from 21 x 21 to 41 x 41 pixels produce good results at acceptable execution times Patch size This selection refers to the dimension of the square patch used to characterize the area sur rounding each data point The choices are limited to 5x5 or 7x7 The default selection is 5x5 Weighting method This selection refers to the method by which the final value is ultimately computed Averaging The denoised value is determined by a simple weighted average of the pixels comprised in the search area This is the default setting Linear regression The denoised value is determined by weighted linear regression of the pi
34. age is not georeferenced or if their georeferencing projection is different the correlation must be processed with the Gridded Output unchecked see Sec 10 If both the master and slave image have an identical map projection ground footprint can be different but projection have to be the same the Gridded Output box can be either checked or unchecked 3 Output grid Select the output footprint of the warped slave Usually the master image or a subset of it is selected here However for georeferenced images it is sometime desired to keep the ground footprint of the slave image in which case select the slave image to defined the output ground grid Note that in case of non georeferenced image the output grid must be defined from the master or subset of it 4 Warping options e Dense warping from the correlation If selected the slave will be warped according to the correlation map values around each pixel of the slave image Conceptually this option corresponds to an independent warping of each pixel according to the correlation map values Note that it is recommended first to clean the correlation from outliers and replace NaN values with plausible values e g median filtering e Polynomial fit from the correlation This option fit a polynomial surface to the correlation maps and warp the slave image according to this polynomial surface fit Please refer to Sec 11 2 for 37 information about the polynomial fi
35. and the GCPS Optimization It represents the weight of the GCP OPTT DX DY DZ are used for the GCPS Optimization only See Sec 8 Sec 9 1 for more details 8 GCPS Image 1 txt Notepad BEE Fie Edit Format View Help File generated the wed Mar 15 18 57 51 2006 GCPS generated from Tied point file D studycase tpts_Raw_Img2_with_ortho_iImgl pts GeoReferenced image D XStudyCase wortho Image 1 j DEM D XStudyCasexXDEM values Easting Northing Altitude x Y weight opti dE dN dA Opti dE dN and dA are only used in Gcps optimization 34 313134931 1173 68518739 2083 9954 1 0000 0 0000 34 382102952 834 15819919 3348 1257 1 0000 0 0000 348595608 1025 86037987 1367 5355 1 0000 0 0000 116 467548671 307670261 1041 29357648 6282 10458 1 0000 0 0000 116 456503467 353732243 891 91973868 7252 4593 1 0000 0 0000 Figure 6 GCPS text file format GCPS Optimization Even with all the care taken during manual tie points selection converted then to GCPS the orthorectified image usually presents a misregistration with the reference image at the GCP s location To get a better co registration GCPS are refined using the following process 1 2 The raw image EO aerial Look Angles satellite are computed using the GCPS The raw image is ortho rectified and correlated with the reference image At each GCP location the GCP ground coordinates are corrected by the ground offset found between the
36. arameters may not be appropriate for a given data set In these cases the results will be sub optimum and it becomes necessary to modify the optional parameters so as to achieve optimum denoising Any combination of parameters is possible with the following two exceptions Minimum weight value and Minimum of weights These two parameters only take effect if the user has selected Linear as the weighting method Otherwise they are ignored and changing their values will not affect the results To speed up parameters adjustment during trials and errors note that a spatial subset of the image to be filtered can be selected Then the filter is only applied on this image subset 11 2 Image Detrending This tool Tools Image Detrending removes a polynomial trend in an image In essence a polynomial surface is fitted to the image and then removed from the image By default the polynomial fit is done on 33 the entire image It is possible to spatially subset the area onto which the fit should be computed either from the ENVI spatial subset tool and or through the ROI tool o Select the file to remove trend from ES Select Input File File Information Host Intel Projection Equidistant Cylindrical Pixel 4 045619 Meters Datum D Sphere Mars Wavelength None Upper Left Comer 454 1070 Description Create New File Mon Oct 6 15 48 52 2014 Spatial Subset Full Scene Select By File u
37. artifacts in the cross track direction whereas a CCD artifact will cause along track stripes Image to apply the correction to if different If the corrections are meant to be applied to a file different than the one they are determined from select it accordingly It must be of the same size with the same number of bands that the file used to determine the correction A typical case is when a denoised and smoothed correlation file is used to determine the stripes correction but the correction is applied to the raw correlation file If this field is left empty the correction will be applied to the file from which the correction is determined Corrected File Select the filename to create if you want to save it to the disk Otherwise leave the field empty for in memory computation but keep in mind the size of the image in regards to the available dynamic memory Click OK After a short computing time a transformed image with the undulations aligned either horizontally or vertically will be loaded in memory Select the file and select the spatial subset that will be stacked to determine the correction The same spatial subset will be stacked on each selected band Click OK The output image will be the original file with the selected band corrected The correction applied to the bands is appended as additional bands at the end of the file The non selected bands remain unchanged 11 6 Vector Field This tool
38. ata file satellite or IO file aerial Select the data file corresponding to the image to orthorectify 3 EO or GCPS file aerial or GCPS file satellite e Aerial image Select the EO file or the GCPS file In case of GCPS file the EO will be computed prior to the matrices computation e Satellite image Select the GCPS file If not selected the orthorectification will only use the ancillary data file to orthorectify the image The accuracy will therefore depends on the satellite ancillary data accuracy 4 DEM Select the DEM file to account for the topography The file must have a valid map information and can be in any projection If not entered the orthorectification will take place assuming a flat topography at altitude 0 above the ellipsoid WGS 84 24 n Orthorectification Resampling Input Select mage to orthorectfy Not Selected Select Ancillary Data File Not Selected GCPS File optional Not Selected DEM optional Not Selected Map Grid From Raw Image From Georeferenced Image Manual Edit f TI Not Defined Save wrapping matrice Not saved Resampling Kemel Sne Options Output Result to File Memory Enter Output Filename Choose Figure 8 Orthoresampling tool 5 Map Grid Define the projection and ground grid of the orthorectified image Note that the datu
39. athToCosi lt IDL_DEFAULT gt export IDL_DLM_PATH pathToCosi cosi modules lt IDL_DEFAULT gt export PATH PATH pathToCosi usgs export DYLD_LIBRARY_PATH DYLD_LIBRARY_PATH pathToCosi cosi modules Note 1 You need to update the full path of the first line of code above source Applications exelis envi50 bin envi_setup bash with the correct path of your system Note 2 lt IDL_DEFAULT gt must be typed verbatim Note 3 The single quotes for IDL_PATH and IDL_DLM_PATH are mandatory Save the file and close it If you are using an ENVI version different than ENVI 4 7 you need to create a symbolic link to an IDL library a Locate the relevant idl library Depending on your ENVI version it will have a different name and should be something like libidl 8 0 dylib W for ENVI 4 8 libidl 8 2 dylib for ENVI 5 0 libidl 8 3 dylib for ENVI 5 1 The path to this library is for instance Applications ezelis idl82 bin bin darwin z86 64 for a standard installation of ENVI 5 0 This path will depends on your own setup b In a terminal type cd pathToCosi cosi modules ln s path to libidl x x dylib libidl 7 1 dylib 3 For Mars imagery users only 5Replace path ToCosi with full path and replace path to libidl x x dylib with full path and name of the library identified in a 11 e USGS Isis 3 software download and installation See Isis install Basic guideline ISIS installation is a two steps process First you
40. atic if they are not accounted for Note 2 If the calibration report is not available the IO can still be built but the lenses distortions principal point offset and fiducial points measures will not be accounted for The focal length the scanning 15 resolution and the fiducial points coordinates in pixel are needed The principal point is assumed to be at the crossing of the lines joining the opposite fiducial points 4 2 Exterior Orientation amp Exterior Orientation DER OK Select Interior Orientation D NStudyCaseM Image 1 t t CERES Select GCPS File D sStudyCaseNGCPS Image 1 t t Queue Dutput Select Exterior Orientation D StudyCase EO_Image_1 tst Figure 4 Exterior Orientation tool This function Aerial Imagery gt Exterior Orientation computes the Exterior Orientation EO of the camera Fig 4 It describes the position and the angular orientation of the camera in the ground coordinates system at the time of exposure It is composed of the spatial position which corresponds to the camera optical center coordinates i e Easting Northing Altitude and the angular orientation which is composed of three rotation angles w k and may be seen as the roll pitch and yaw of the focal plane These six parameters are determined using space resection by collinearity Ayoub et al 2009 Wolf amp Dewitt 2000 1 Interior Orientation Select the file obtained during the Interior Or
41. ch point the optimization window size should be kept in mind when picking tie points Pay attention to the points surrounding Are features recognizable between the two images Try to select points whose neighborhood contain easily identifiable features or patterns Are there any tem poral decorrelations man made changes shadowing differences Prefer areas of low topography to minimize uncorrected stereoscopic artifact It is not necessary to select tie points precisely as the optimization will correct them With the frequency correlator the maximum placement error allowed on the initial GCPS will correspond to half the correlation window size With the statistical correlator a search range will have to be defined Tie points to GCPS l Convert Tied Points to GCPS E ex Select Tied Points File D StudpCase tpts_Raw_Img2_with_Ortho_Img1 pts Bares Select Reference Image D StudyCase Ortho_Image_1 mem Select DEM File optional D StudyCase DEM Select Offset Field optional D NStudyCaseNE xtemal Displacement Map Output Select GCPS File D StudpCase GCPS_Image_2 txt Figure 5 Tie points to GCPS transformation tool This function Tie Points GCP Tie points to GCPS converts a set of tie points into GCPS Fig 5 20 5 Tie Points File Select the file containing the tie points between the two images The file must be of the form x master y master x slave y slave in pixel This fil
42. commended to use the Sinc kernel for an improved resampling quality and ultimate correlation Default kernel size is 15 pixels which you can adjust through the Option button The kernel size represent the number of sinc lobes computed Larger kernel window size provide a better resampling but are longer to compute Improvement in the resampling quality for kernel size larger than 15 pixels are negligible 8 Output Select the file name of the orthorectified file to create You can save the file in memory only if you want 10 Correlation and Displacement Measurements 8l Correlation Select Pre Event Image C StudyCase Ortho_Image_1 Select Post Event Image C StudyCaseSOrtho Image 2 Correlator Engine Frequential Options Dutput Select Correlation File C StudyCase DisplacementMap Figure 9 Correlation parameters selection tool This function Correlation correlates two images and provides a map of the relative displacements Fig 9 1 Pre event Image Select the first image of the pair This image is considered the reference 2 Post event Image Select the second image of the pair The correlation result provides a displacement field using the convention eastward and northward positive This displacement field is the horizontal ground displacement that should be added to the pre event image to retrieve the post event image 3 Correlator engine Select the correlator engine Currently
43. corporate Software with other source code developed by LICENSEE Incorporated Work for the sole purpose of using Software for research internal to LICENSEE and not for any other redistribution LICENSEE may not distribute any Incorporated Work outside of LICENSEE and specifically LICENSEE may not provide Software or any Incorporated Work under an open source license such as the Gnu Public License www gpl org If the creation of an Incorporated Work would require LICENSEE to distribute Software under an open source license then LICENSEE agrees not to make such incorporation 6 Software is experimental in nature and is being licensed as is The license of COSI Corr does not include any technical support or documentation 7 LICENSEE hereby represents and warrants that it is a not for profit entity 8 CIT represents and warrants that it has the right to license Software 9 LICENSEE agrees that any person within LICENSEE utilizing Software will be advised of and is subject to the conditions in this Agreement 10 NO WARRANTY SOFTWARE IS PROVIDED AS IS WITHOUT WARRANTY OF ANY KIND INCLUDING ANY WARRANTIES OF PERFORMANCE OR MERCHANTABILITY OR FITNESS FOR A PARTICULAR USE OR PURPOSE AS SET FORTH IN UCC 23212 2313 OR FOR ANY PURPOSE WHATSOEVER HOWEVER USED IN NO EVENT SHALL CIT BE LIABLE FOR ANY DAMAGES OR COSTS INCLUDING BUT NOT LIMITED TO INCIDENTAL OR CONSE QUENTIAL DAMAGES OF ANY KIND INCLUDING ECONOMIC DAMAGE OR INJURY TO PROPERTY AND
44. dth odd fields and Position on fault buttons The simple arrow button moves the box center to the next pixel on the fault whereas the double arrows button moves to the next 20ieth pixel on the fault 43 AV 1 North South Chichi_Displacement Be File Options View Stack 1 Stack 8 _Add Remove 44 Position on Faut P pp x 278 v 128 Stack Length odd 101 Stack Width odd 31 Accept 4 Band p Curent Band North South Left Fit From 46 To 10 RightFit From 5 To 50 Fit Stack Offset 7 27430 Sigma 0 283568 Figure 24 Profiles stacking tool Stacking Boxes Visualization There are two visualization possible e View Stack Visualization displays the spatial location and extent of the stack i e the stack boxes Open the ENVI ROI tool to display the stack boxes Note that you can delete the stack boxes ROI without interfering with the stacking profile tool Close all open ROIs before visualizing the stack boxes as open ROIs will be first deleted e View gt Offset Visualization extracts the slip on the fault from all the stacks and plot them Select the slip component you would like to display band you can also display the standard deviation of each estimated slip along the fault as well as the norm of the slip norm of all displayed bands Profile projection By default profiles are in the file
45. e is typically generated by the Tie Points Tool Sec 7 1 but you can edit it manually Reference Image Select the image used as a reference master during the tie points selection The image must have a map information and is typically an orthorectified image The geographic coordinates will be retrieved from its map information DEM File Select a DEM with a valid map information to retrieve the altitude of the GCPS If not entered the altitude will be set to 0 Offset field If selected this field must receive a file whose first and second bands contain a dis placement map of the area in East West and North South direction respectively a correlation map typically The displacement found at the GCP location is retrieved and added to the GCPS file This information will be used in the GCPS optimization Sec 8 as this displacement will be accounted for during the optimization For example a SPOT based displacement map can be used to account for the ground displacement at GCP location while co registering aerial images Ayoub et al 2009 GCPS File Select the name of the GCPS file to be created The format of the GCPS file created is Fig 6 longitude decimal degree latitude decimal degree alti tude meter X pixel Y pixel SNR 0 to 1 OPTI 0 or 1 DX meter DY meter DZ meter SNR set to 1 by default can be changed manually if needed and is used during the orthorectification
46. e studyCase2 master tif 2 home johnMclane studyCase3 master3 tif 2 500 2564 758 6225 home johnMclane studyCase master tif 1 500 2564 758 6225 e Slave file This file is mandatory Same layout and options as the master file Correlation Options file This file is optional If not used the correlation parameters by default will be applied Frequential correlation using a 64x64 pixels correlation window size and a step of 16 pixels The layout for customized correlation parameters are the following Frequential Correlator frequency winMaxX winMaxY winMinX winMinY stepX stepY nbRo bustIteration MaskThreshold resampling grid See Sec 10 1 for details 29 Statistical Correlator statistic winX winY stepX stepY seachX searchY grid See Sec 10 2 for details For instance frequency 64 64 82 82 16 16 4 0 90 1 frequency 64 64 64 644440900 statistic 32 32 161677 1 statistic 10 10 2 2 10 10 0 Correlation filenames file This file is optional If not entered the correlation file will be stored in the slave file directory and will be named correlation masterFileName vs slaveFileName id with id being the correlation number of the batch If entered the file contains the full path of the correlation file name one file name per line Master Slave Correlation Options and Correlation Filenames files must have the same number of lines However there is one exception It is possible for Master Slave and Correlati
47. ed to any other change detection application We describe below the successive steps to achieve precise co registration and derive deformation measurements We assume here that we have two images bracketing a seismic event Before correlation the images must be cleaned from geometric artifacts such as topography and co registered precisely 1 Define the Interior Orientation aerial or Ancillary data satellite of the two images Sec 4 1 5 1 2 Orthorectify the pre earthquake image a Construct a Ground Control Points GCPS file to refine the pre earthquake image absolute geolocation and coregistration to the Digital Elevation Model DEM GCPS are defined either with GPS campaigns or by taking tie points between the image and a geolocalized reference orthorectified image shaded DEM digitalized high resolution map Sec 7 1 The tie points are then converted into GCPS Sec 7 2 using the georeferencing parameters of the reference image and a DEM Those GCPS can be optimized if necessary Sec 8 b Compute the mapping matrices to transform the raw pre earthquake image into an orthorectified image and resample it Sec 9 3 Orthorectify the post earthquake image a Select tie points between the post earthquake image and the orthorectified pre earthquake image Sec 7 1 b Convert these tie points into GCPS Sec 7 2 c Optimize the GCPS of the post earthquake image in order to precisely co register the post earthqua
48. eir measurements which are read from the calibration report Fig 2 Once the points are selected save the file File Save Points to ASCII Note in the recent versions of ENVI the fiducial points selection tool is embedded in the ENVI Build RPCs GUI When opening the Aerial Imagery Interior Orientation Fiducial Points Selection Tool the Build RPCs GUI will open Click on the Select Fiducials in Display button to access the fiducial selection tool Once the points are selected save the file File Save Points to ASCII close the Build RPCs GUI and move to the Interior Orientation Setup 41 Ortho Build Interior Orientation ES File Options Help AAA ee eM EEI Fiducia x 703 9460 3 Imagex 59450 S Image v 818 00 Fiducial Y 103 9380 gt Review amp Comment E Secure f sign Advanced Editing BS HowTo Number of Selected Points 1 Show List RMS Error N A Delete Last Point VII Principal Points and Fiducial Coordinates 2 180 Positions of all points are referenced to the principal point of autocollimation PPA as origin The diagram indicates the orientation of the reference points when the camera is viewed from the back or a contact positive with the emulsion up The data strip is to the left d a t a s t r i p s i d e 1 09 4 270 X coordinate Y coordinate Al
49. ement between two patches Usually in noisy images or when large displacement are expected the initial window is setp up to large size In theory the window size should be at least twice the expected displacement but in practice we recommand a larger ratio i e use a 128 or 256 initial window size with an expected displacement of 15 pixels Once the initial displacement is estimated a second final correlation is operated to retrieve the subpixel displacement It is customary to select for the final window size the smallest size that will provide a reasonable amount of noise from experiment a window size of 32x32 pixels is the minimum and a window size of 32x32 or 64x64 usually yields good results with good quality images as it will increase the density of totally independent measurements The parameters for the frequency correlator are Fig 10 1 Window Size Initial Size in pixels in X and Y direction of the initial sliding window that will estimate the pixelwise displacement between the images The size is a power of two 2 Window Size Final Size in pixels in X and Y direction of the final sliding window that will compute the subpixel displacement between the the images The size is a power of two 3 Step This parameter determines the step in X and Y direction in pixels between two sliding windows If the step is greater or equal to the final window size then all measurements are independent 4 Robustness Iterati
50. endent the sigmas must be weighted accordingly in order to correctly reflects the sigma on the offset measures 11 8 Manual Stacking Profiles This function allows the user to extract stacked profile from an image usually a correlation map The principle is similar to the one described in the previous section Sec 11 7 with a somewhat lighter approach and a less seismo tectonic feel Basically the user doesn t need to define a fault trace and select directly the profile of interest using the ENVI ROI tool The steps to extract stack profiles are the following 2 Band Math b1 Memory3 o amp O 1 Band Math b1 Memory3 ole ls File Overlay Enhance Tools Window File Overlay Enhance Tools Window ROI ID Region 1 Red 174 points Stack size pixels 3 Image Band V East West Noth Souh Z SNR E Display Stack in ROI E Plot Min Max Stack Figure 25 Manual stacking tool 1 Open the image to extract measurement from 2 Using the ROI tool and using the polyline selector ROI Type gt Polyline draw the profile of interest Fig 25 top left panel If you want to do several independant profiles you need to create a New Region for each of them 3 Open the Manual stacking tool from COSI Corr gt Tools gt Stacking Profiles Manual stack Fig 25 bottom right panel 45 e Select the image display ID of interest e Roi ID Select the ROI i e profile of interest
51. for a process to be queued the data to be selected may not exist yet for example when it is supposed to be computed in a task queued before Depending on the type of data to be selected ENVI file Click on Cancel A regular file selector will be displayed Enter the name at the correct path location of the file to be created Note that in this situation spatial and spectral subsetting are not possible If no regular file selector is displayed the file must then exist at the current time Other Enter the name at the correct path location of the file to be created Do not open more than one COSI Corr window at a time except for the queue manager window as crash will occur otherwise 47 In case of an ENVI blocking crash due to more that one COSI Corr window opened bug enter in the IDL command line retall and press enter It will most of the time unblock ENVI If not you may have to restart ENVI 48 References S Leprince S Barbot F Ayoub and J P Avouac Automatic and Precise Ortho rectification Coregistra tion and Subpixel Correlation of Satellite Images Application to Ground Deformation Measurements IEEE Trans Geosci Remote Sensing vol 45 no 6 pp 1529 1558 2007 F Ayoub S Leprince and J P Avouac Co registration and Correlation of Aerial Photographs for Ground Deformation Measurements ISPRS Journal of Photogrammetry and Remote Sensing vol 64 no 6 pp 551 560
52. he ground footprint of the display will be determined by the first data entered Vector Tool Select Processing Tool Gui The vector field graphic options available are the following Fig 23 e Graph Title Enter the title of the vector field display e Maximum vector value Enter the maximum value of the displayed vectors Vectors of superior values won t be displayed e Ratio Arrow Length Ratio to control the length display of the vectors e Unit Enter the unit name that is displayed on the vector field legend e Vector Field Options The list displays all the data entered on the current display Select the entry of interest to have access to the following options Vector Field Name Select the name that will be displayed in the list Average Window Size Option available only to ENVI data files Determines the window odd size centered on the vector location to average the values in the file 41 A 1 North South Memory6 E x ZI Available Bands List a m Ed File Overlay Enhance Tools Window 8 Memor o East West 9 North South o SNR o East West correction 3 Nodh South correction GH Map Into ConelationSeismo gt East West 2 North South J SNR p Map Into GrayScale RGB Color Selected Band North South Memory6 Figure 22 Destripping tool corrected image Step Option available only to ENVI data files Step in pixel bet
53. hnique discussions and feedbacks from other COSI Corr users Do not change any file name folder name and folder organisation inside path ToCosi If you are not planning on using Mars imagery you can delete but are not obliged usgs folder and cosi corr envi hirise toolkit sav SM ENVI File Basic Tools Aerial Imagery gt Satellite Imagery gt Tied Points GCPS gt Correlation Tools About Cosi Corr Figure 1 Example of the COSI Corr menu inserted in ENVI between the Basic Tool and Classification top level menus 2 4 Getting Help To ask for information help report a bug or a suggestion please first browse the COSI Corr forum http www tectonics caltech edu forum as the problem you are facing may have been already reported Shttp isis astrogeology usgs gov documents InstallGuide index html Replace pathToCosi with full path 12 If you do not find an answer do not hesitate to post your questions comments on the forum To contact the COSI Corr team directly you can also send an email to cosicorr helpQ gps caltech edu We apologize in advance for the inevitable bugs and ask you to send us a clear report of the problems you may encounter 3 Introduction A Typical Processing Chain The driving motivation for implementing COSI Corr was to set up a tool that retrieves co seismic ground displacements from pre and post earthquake images Although the description is aimed at seismo tectonics it can be appli
54. ied to a reference image as the ancillary data are accurate enough to locate them geographically Points will be converted to GCPS prior to optimization This option can be used with SPOT 5 but is not recommended with SPOT 1 4 and ASTER images Unlike the tie points file pixels coordinates must be expressed in a coordinates system where the first pixel coordinates are 0 0 Note that the weighting of the GCPS the OPTI flag and the DX DY and DZ fields are only available through the use of a GCPS file and not a tie points or ICP files 6 Optimization Options a Nb Iterations Number of loops that will be executed to optimize the GCPS 5 loops are usually NA 0 XI A enough to reach stable convergence If the optimized GCPS file report shows that the convergence is not reached the process should be continued Continuation of the process can easily be done by giving as GCP input file the output file where convergence is not reached Resampling kernel Select the resampling kernel that will be used to resample the raw images patches This option is similar to the one described in Sec 9 1 Correlator engine Select the correlation method used to correlate the patches and retrieve the displacements to correct Usually a window size of 128 or 256 pixels is used It will allow for a good co registration on the long wavelengths The statistical correlator is advised when the reference image is the shaded DEM whereas the
55. ientation of the camera Sec 4 1 2 GCPS File Select the file containing the GCPS This file can be obtained from Sec 7 2 or edited manually It is an ASCII file which presents data in an array form One GCP per line with a line composed of longitude decimal degree latitude decimal degree altitude meter X pixel Y pixel SNR 0 to 1 other SNR represents the weight of each GCP in the global EO computation The file must contains at least three GCPS 3 Exterior Orientation Enter the name of the Exterior Orientation file to be created and click OK The file will contain the six EO parameters longitude degree latitude degree altitude meter w radian radian radian Note that is given with the North as a reference and can be seen as the sum of the aircraft azimuth and yaw The EO file is then used during the image orthorectification Sec 9 5 Satellite Imagery Specific 5 1 Ancillary File This function Satellite Imagery gt Ancillary File Satellite to study gt rearranges the ancillary data of a satellite image into a common file format that will be used afterward in COSI Corr This ancillary file contains the positions attitudes and look directions of the satellite while acquiring the image and other information such as the number of lines and columns nominal ground resolution 5 2 Satellite specifics ASTER Imagery The level L1A is required The ASTER hdf file is expected as in
56. images The process is iterated with the corrected set of GCPS until convergence of the ground offset correction 21 This function Aerial Imagery or Satellite Imagery GCPS Optimization GCP Optimization opti mizes a raw image GPCS with respect to a reference orthorectified image to achieve a good co registration Fig 7 l GCPS Optimization Select All Input B Cancel Select Image D StudyCaseXRaw Image 2 Queue Select Reference Image D StudpyCase Ortho_Image_1 Select DEM File D StudpCase DEM Select 10 File D StudpCase I0_Image_2 txt Select GCPS Tied Points File D 4StudyCasettpts_Raw_Img2_with_Ortho_Imgl pts Nb Iteration 5 Resampling Kernel Sinc Options Correlator Engine Frequential Options v Weight GCPS with Correlation SNR v Dynamic Display of Optimization Output Select Optimized GCPS D StudpCase O ptimized_GCPS_Image_2 txt Figure 7 GCPS optimization parameters selection tool 1 Raw Image Select the raw image whose GCPS are going to be optimized 2 Reference Image Select the orthorectified image onto which the raw image will be co registered This image corresponds generally to the first orthorectified image of the pair a shaded DEM or an external orthorectified image The reference must be georeferenced in the UTM projection 3 DEM Select the DEM that will be used to correct the topographic effects during the optimization If selected the DEM m
57. isk Otherwise leave the field empty for in memory computation but keep in mind the size of the image in regards to the available dynamic memory Click OK After a short computing time a rotated image with the undulations aligned vertically will be loaded in memory Select the file and select the spatial subset that will be stacked to determine the correction Fig 21 The same spatial subset will be stacked on each selected band Click OK 39 The output image will be the original file with the selected band corrected The correction applied to the bands is appended as additional bands at the end of the file The non selected bands remain unchanged Fig 22 11 5 2 Automatic Orientation 1 10 11 Image to define correction from Select the bands usually only the EW and NS bands from which the correction will be defined Ancillary file of one image Select the ancillary file of the image causing the undulations to be removed GCPS file if any Select the GCPS file if any that was used to orthorectify the image This is an optional parameters DEM file if any Select the DEM file if any that was used to orthorectify the image Attention the DEM must be valid on the entire image area This is an optional parameters Stripes undulations direction Select whether the artifacts to removed are oriented cross track or along track For example attitude undulations will cause
58. ke image to the orthorectified pre earthquake image Sec 8 d Compute the mapping matrices to transform the raw post earthquake image into an orthorectified image and resample it Sec 9 4 Correlate the two co registered and orthorectified images The result will be a three bands file con taining the E W displacement map positive toward the East the N S displacement map positive toward the North and the SNR assessing the quality of the measure Sec 10 4 Aerial Imagery Specific Film based aerial images must be scanned with a high spatial and radiometric resolution to accurately retrieve the film s information A radiometric resolution of at least 8 bits 10 12 recommended a geometric resolution of 5 to 15 um 5000 dpi to 1700 dpi and a stability of around 2 3 um are desired Zeiss and Leica for example provide suitable aerial images scanners It is recommended to scan in grayscale B amp W the negative and not the photo paper print 13 4 1 Interior Orientation The Interior Orientation IO of the camera gives a mathematical representation of the camera geometry and distortions This step is accomplished with the help of the camera calibration report which is normally obtained on demand and follows the classical photogrammetry techniques Wolf amp Dewitt 2000 The Aerial Imagery Interior Orientation Fiducial Points Selection Tool function allows to select the fiducial points on the image and to enter th
59. l at the same location in the other bands selected will be changed too by their respective replace value 11 5 Destripe Image This tool Tools Destripe Image allows you to remove parallel stripes and undulations in an image A typical use for this tool is the removal of undulation artifacts in a correlation image due for example to an uncorrected attitude like an oscillating pitch or a CCD array artifact in ASTER or SPOT images The main idea is to average the artifact by stacking and subtracting the average to the image Two functions are available and are described below The Manual Orientation allows to destripe any image but the user need to supply manually the rotation angle necessary to align vertically the undu lations stripes to remove The Automatic Orientation defines automatically the affine transformation necessary to align the undulations stripes before performing the stack The transformation is defined from the ancillary file and GCPS file optional of the image responsible for the undulations stripes 38 5I 1 North South CorrelationSeismo B x 7I Available Bands List D x CorelationSeismo O East West North South c SNA a Map Info C GrayScale RGB Color C R Notth South CorelationSeismo Gg NorhSouth CorrelationSeismo C g SNR CorelationSeismo Dims 630 x 594 Floating Point BSQ LoadRGB Display 1 Select Image to define conection from D Correlation
60. licking on a band name in the band list causes the parameter controls to be updated with that band s particular parameter set NOTE The user must supply a noise parameter for each band since this parameter has no default value All other parameters may be left at their default settings if so desired 31 4 Filtered bands file Select the name of the filtered bands output file The filtered bands are automat ically assigned the same names as the originals but in addition have NLMfiltered appended to the end of them In addition the header file will list the filter parameters for each band NOTE During processing the ENVI IDL user interface is unresponsive A progress bar is displayed that increments after each band has been filtered 11 1 2 Filter Parameters Fig 12 H noise parameter This number is used to control the degree of denoising and is proportional to the standard deviation of the noise A common value for H is between 0 5 and 2 times the standard deviation of the noise and it depends on the other parameters selected The stronger dependencies are on the weighting type Standard Bisquare or Modified Bisquare and on whether the center data point is omitted or not in the advanced parameters With the default parameters a value of H close to 1 6 times the noise estimated standard deviation is a good estimate This parameter does not have a default value Therefore the user MUST supply a noise parameter for e
61. m of the projection must be the same as the datum of the DEM if used Three options are available to define the grid e From Raw image The ground footprint is defined from the raw image size and susbet if a Spatial Subset was defined during the image selection e From Georeferenced image Select an existing georeferenced image to define the cartographic projection and ground footprint and resolution It is possible to Spatial Subset the georeferenced image to reduce the ground footprint This option is useful when orthorectifying the second image of a pair that needs to be correlated Selecting the orthorectified first image of the pair guarantee that ground footprint and resolution are identical e Manual Edit Select modify manually the grid Note In the Grid Parameters window the button Adjust grid to be multiple of resolution forces the grid corners to be multiple of the ground resolution selected This action guarantees that all orthorectified image of the same resolution can be aligned exactly pixel wise 6 Save warping matrice If desired the mapping between the raw image and the orthorectified image can be saved 25 7 Resampling Kernel Three resampling kernels are available Bilinear Bicubic and Sinus Cardinal Sinc The bilinear and bicubic kernel do not accept any parameters and are somewhat faster than the Sinc The Sinc is a more precise resampler than the two other kernels It is re
62. mera system enter the Exterior Orientation file of the slave image 5 GCPS File optional Enter the GCPS file that was used if any to orthorectify the slave image 6 DEM optional Enter the DEM that was used if any to orthorectify the slave image Usually the slave DEM is the same as the master DEM but doesn t have to 46 12 Master image Parameters Pushbroom Camera Frame Camera Select Ancilary Data File Not Selected Select GCPS File optional Not Selected Select DEM optional Not Selected Slave Image Parameters 9 Pushbroom Camera Frame Camera Select Ancilary Data File Not Selected Select GCPS Fie optional Not Selected Select DEM optiona N Output Result to File Memory Enter Output Filename Choose Figure 26 Epipolar projection tool Correlation File Enter the correlation file that will be projected into the Epipolar and Perpendicular Epipolar direction Select the output filename The output will contain 5 bands Epipolar component Perpendicular Epipolar component SNR component copy of the original SNR band E W direction of the Epipolar direction N S direction of the Epipolar direction Miscellaneous A queue manager is available in COSI Corr to allow batch processing An unlimited amount of tasks can be queued and will be processed on a first selected first processed basis When selecting data
63. omatically Worldview Imagery The level 1B Basic is required Note that only full scenes not susbets are accepted The files eph att geo and imd or the xml will be needed and must be located in the same folder only one of these 4 files need to be entered in the auxiliary file field the other ones being retrieved automatically 6 Mars Imagery Specific 6 1 Ancillary File HiRISE Imagery The hi socet pl script will generate the raw image and a keywords lis which contains all the telemetry and geometric information of the image acquisition The keywords lis is needed to generate the COSI Corr ancillary file Please see Sec 6 2 for more details on pre processing HiRISE image CTX Imagery The mroctz4socet pl script will generate the raw image and a keywords lis which contains all the telemetry and geometric information of the image acquisition The keywords lis is needed to generate the COS Corr ancillary file of the CTX image 6 2 HiRISE CTX general process pre COSI Corr Before HiRISE and CTX images can be used in COSI Corr the raw imagery need to be processed in a format compatible with COSI Corr This is done using ISIS and USGS scripts which will for HiRISE e Reconstruct the full image from the 10 images stripes These stripes were acquired by each of the 10 CCD arrays on the focal plane since about 3 years only 9 CDD arrays are operating e Extract of the telemetry and geometry of the image acquisiti
64. on Number of times per measurement the frequency mask should be adaptively re computed The mask contributes in reducing the noise on the measurements 2 to 4 iterations is satisfying in most cases Leprince et al 2007 27 5 Mask Threshold Allows the masking of the frequencies according to the amplitude of the log cross spectrum A value close to unity is appropriate in most cases See Leprince et al 2007 for more details Resampling Patches to correlate are relocated from sinc resampling This option theoretically eliminates most of the biases at the sub pixel scale If used the processing time is greatly increased on average by a factor of 10 However on noisy images its usefulness has been noticed only on a very few occasions Grided Output Check this option if you want to obtain a displacement map with the top left corner coordinates to be integer multiple of the ground resolution This is mostly useful when several corre lation of the same area need to be overlaid or mosaiced If unckeck the top left corner coordinates of the displacement map will be identical to the top left corner coordinates of the master image 10 2 Statistical Correlator 8 Statistic Correlator Window Size Xx 2 Ue 32 Step X fie Y fie Search Range X fio AE fo Grided Output Iv _OK Cancel Figure 11 Statistic correlator parameters The parameters for the statistical correlator are Fig 11 l 2
65. on e Convert the reconstructed image from ISIS format cub to a binary format interpretable by ENVI In practice these steps are carried out from the following steps 17 1 Get the 10 or 9 red band stripes of the HiRISE image of interest These stripes can be either obtained from a HiRISE team member in the format of balance cub these balance cub stripes are unfortunately not public so one needs to contact a HiRISE PI or generated from the EDRs publicly available from the HiRISE website http hirise lpl arizona edu Refer to ISIS documentation for details See paragraph Batch processing of EDR processing The main difference between the two processing is a better color balancing between stripes with the balance cub compared to the norm cub 2 Run hi4socet pl on the balance cub list or norm cub list Let s assume that EDRs of HiRISE image ESP 028087 1890 have been downloaded from the HiRISE website and that the stripes have been reconstructed following the ISIS recommendation We ll have the following files ESP 028087 1890 REDO norm cub ESP 028087 1890 RED1 norm cub ESP 028087 1890 RED2 norm cub ESP 028087 1890 RED3 norm cub ESP 028087 1890 REDA norm cub ESP 028087 1890 RED5 norm cub ESP 028087 1890 RED6 norm cub ESP 028087 1890 RED7 norm cub ESP 028087 1890 REDS norm cub You ll notice that we only have 9 stripes instead of 10 as this image was acquired after CCD9 failure Now run the
66. on Options files to have only one line although the other files have more lines This indicates that the single line parameters is to be applied to all correlations of the batch For instance if Master file has one line and Slave file has 10 lines there will be 10 correlations one master image to be correlated with the 10 slave images Similarly if the correlation file has only one line the same correlation parameters will be applied to all correlations 10 3 2 Batch Correlation execution The batch correlation can be executed through IDL ENVI command line ENVI cosi batch correlation masterFile slaveFile CORR corrFile OUT outFile NO OPEN no open For instance ENVI gt cosi batch correlation home johnMclane studyCase master txt home johnMclane studyCase slave tat CORR home johnMclane studyCase correlations tzt OUT home johnMclane studyCase correlationNames tat By default the procedure opens the master slave and correlation files in ENVI If set the NO_OPEN key word does not open the files to set the keyword enter in the commande line NO_OPEN 1 Default is NO_OPEN 0 Alternatively the batch correlation can be executed through the COSI Corr GUI COSI Corr gt Corre lation gt Batch Correlation which will ask successively for the Master Slave Correlation Options and Correlation Filename files If not providing a Correlation Options or Correlation Filename files just click Cancel 11 Tools
67. osi usgs export LD LIBRARY PATH LD LIBRARY PATH pathToCosi cosi modules 10 Note 1 You need to update the full path of the first line of code above source usr local exelis envi50 bin envi_setup bash with the correct path of your system Note 2 IDL DEFAULT must be typed verbatim Note 3 The single quotes for IDL PATH and IDL_DLM_ PATH are mandatory Save the file and close it Mac OS Please note that the Mac version of COSI Corr is new and has only been lightly tested You need to update your startup shell script to indicate to the operating system where the necessary COSI Corr files are Most Mac OS X versions use the bash shell by default although several other shell are available bash csh zsh etc If you don t know what is your default shell you can find out by typing in a terminal the following ps p Examples on how to update you startup shell script are given for the bash shell If you are using a different shell please refer to its documentation to create environment variables Edit your bash profile file using a text editor The bash profile file is usually located in your home directory e g Users johnMcClane Warning the bash profile is a hidden file If the file does not exist you need to create it keep same name bash profile and home directory Edit the bash profile file and add the following at the end of the file source Applications exelis envi50 bin envi_setup bash export IDL_PATH p
68. plication to Ground Deformation Measurements IEEE Transactions on Geoscience and Remote Sensing vol 45 no 6 pp 1529 1558 2007 and if working with aerial images F Ayoub S Leprince and J P Avouac Co registration and Correlation of Aerial Photographs for Ground Deformation Measurements ISPRS Journal of Photogrammetry and Remote Sensing vol 64 no 6 pp 551 560 November 2009 The developers also request that in your oral presentations and in your paper acknowledgements you indicate the use of COSI Corr 1 6 Disclaimer NONEXCLUSIVE NON TRANSFERABLE LICENSE AGREEMENT FOR RESEARCH PURPOSES ONLY FOR COSI Corr Software Co registration of Optically Sensed Images and Correlation The California Institute of Technology CIT will provide you a not for profit institution LICENSEE with the Co registration of Optically Sensed Images and Correlation Software COSI Corr Software is made available to LICENSEE on the following terms 1 Definitions a The Software is defined as the package consisting of the source code and the compiled version of the software that allows for Co registration of Optically Sensed Images and Correlation based on the algorithms described in S Leprince S Barbot F Ayoub and J P Avouac Automatic and Precise Ortho rectification Coregistration and Subpixel Correlation of Satellite Images Ap plication to Ground Deformation Measurements IEEE Transactions on Geoscience and Remote Sensing vol
69. put Although any band can be selected VNIR SWIR TIR it is recommended to use the band VNIR 3N nadir viewing for surface deformation detection 16 Formosat 2 Imagery The level 1A is required Panchromatic and multi spectral images can be pro cessed The METADATA dim file is needed SPOT SPOT5 Imagery The level 1A is required Panchromatic and multi spectral images can be processed Leader lead dat file and Dimap dim format are accepted Panchromatic with CCD correction accounts for the slight misalignment of the CCD arrays in SPOT1 4 The correction is established empirically for each satellite and is currently only available for the SPOT 2 HRV 1 and SPOT 4 HRV 1 instruments SPOT6 7 Imagery The level 1A is required Panchromatic and multi spectral images can be processed Note that only full scenes not subsets are accepted The DIM_xxxx XML file is needed Pleiades Imagery The level 1A is required Panchromatic and multi spectral images can be processed Note that only full scenes not subsets are accepted The DIM_xxxx XML file is needed Quickbird Imagery The level 1B Basic is required Panchromatic and multi spectral images can be processed Note that only full scenes not subsets are accepted The files eph att geo and imd or the xml will be needed and must be located in the same folder only one of these 4 files need to be entered in the auxiliary file field the other ones being retrieved aut
70. r example would be a feature clearly recognizable between the reference image and the raw image during tie points selection but with a surrounding of poor quality content that may bias the correlation if optimized Although rarely used this option can be useful when dealing with heavy snow or heavy cloud cover DX DY DZ are used to account for a ground surface displacement sustained at the GCP location They refer respectively to the displacement in Easting Northing and Elevation in meter currently the Elevation displacement is not used If values are entered the GCP will be optimized in order to co register the images while accounting for the displacement entered at the GCP location e Tie points file This is a file whose format is x ref y ref x raw y raw and is usually generated with the ENVI tie points selection tool Sec 7 1 or edited manually The reference image and raw image used for the tie points selection must be the same as the ones entered in the GCPS optimization windows Tie points will be converted to GCPS prior to optimization Note that if the tie points file is edited manually pixels coordinates contained in the file must be expressed with the convention where the first pixel coordinates are 1 1 to stay consistent with the ENVI points selection process ICP Image Control Points This option is available only for satellite imagery It is a file whose format is z raw y raw The points do not need to be t
71. re 16 shows a ROI red area used to define the polynomial fit from Note that the ROI must be defined before using the detrending tool 4 Once the spectral and spatial subset and optional ROI are selected the main GUI detrending GUI is displayed Fig 17 34 Figure 16 Exemple of area selection through ROI to define the polynomial fit e Decimation step pix The definition of the polynomial fit can involve a lot of memory RAM To limit the memory footprint this field allows to decimate the image prior to fitting the polynomial surface A decimation step of 10 for instance means that only 1 pixel out of 10 in column and row are selected for the definition of the polynomial fit e Polynomial fit degree Degree of the polynomial surface to fit to the image and substract afterward from the image A degree of 1 means that a plane will be defined e Fit iteration This parameters limits the influence of the outliers which can bias the polynomial fit Once the polynomial fit is operated all pixel for which the residual between the image and the fit is larger than the standard deviation of the residuals are filtered out and a new fit is operated on the filtered image This process is operated as many times as defined by the user Note that it is not recommended to set up a large number of iteration as once the largest outliers are removed this process will start removing valid data over filtering e
72. ssor recommended Mars HiRISE CTX users will also need the following lhttp www tectonics caltech edu slip__history spot_coseis index html e ISIS 3 4 3 and up isis astrogeology usgs gov Note that ISIS is only available for Linux and Mac OS e USGS scripts to transform HiRISE CTX raw imagery in Socet Set COSI Corr compliant format hi4socet hinoproj The scripts are provided in the COSI Corr package but user should seek updated codes from the USGS if needed planetaryphotogrammetry usgs gov e HiRISE toolkit from Adam O Connor can be loaded from Exelis website to properly open and read map information of HiRISE images in ENVI The toolkit is provided in the COSI Corr package 2 3 Installation If you have a previous version of COSI Corr installed you need to remove it first Let s assume that you want COSI Corr to be installed in a folder named mySoftware For instance C Users John McClane Documents mySoftware for Windows home johnMcClane mySoftware for Linux Users johnMcClane Documents mySoftware for Mac You can name and choose the location of this folder as you wish Copy the cosicorr lin tar gz Linux or cosicorr win zip Windows or cosicorr mac tar gz Mac depending on your OS in this folder mySoftware Unzip the file A new folder names cosi corr will be created in mySoftware directory C Users John McClane Documents mySoftware cosi corr for Windows home johnMcClane mySoftware cosi corr
73. t options 5 The mapping matrice defined from the correlation map can be saved if needed either on disk or in ENVI memory beware of potential large size of the mapping matrice 6 Select the resampling kernel used to resample the slave image according to the mapping Options are described in Sec 9 1 7 Select the warped slave output type either on disk need to provide a file name or in ENVI memory 11 4 Discard Replace Image Values l Values to filter North South Min value empty for no limit North South Max value empty for no limit Replace filtered values by empty for NaN Ok Cancel Figure 19 Band parameters selection tool for image filtering This tool Tools Filter Image Values allows you to filter and change pixel values in an image based on their values The file can contain several bands Typically this function is used to filter out outliers or values with a weak SNR in a correlation file 1 Select the file and the bands of interest Non selected bands will not be changed 2 For each band selected enter the minimum maximum and replace values Fig 19 3 Select a file name if you want to save the filtered file on the disk or leave the field empty for in memory load Every pixel in the band whose value is smaller than the minimum or larger than the maximum will be assigned the replace value Note that for a pixel in a band changed pixe
74. ted with the ROI tool when mapping the fault 42 O gt i Vector Tool Chi T T T T rT placement Field 1 ce a a Graph Options Graph Title Chi Chi Displacement Fie Maximum Vector Value 20 Ratio Arrow Length D 08D 2 680X 108 Unit Meter Axis Color Black X Background Color White X Vector Field Options SPOT Measures GPS PS Measures D 7 l 1 l l 1 El i L l L L 2 670x108 1 L 31 l 1 n J l 1 1 1 H H y AAA d 1 d J 1 l l 1 l 1 1 1 1 I L l L SAINI NNSS lS IA Sa PRA SSN SSS ACC e He n dante J l Vaan um Ioa O o a el ER AAA 4 then 265X105 2 70X105 2 5X105 2 80X105 MOM UAI RD E eR RRR Vector Field Name GPS Measures Average Window Size Step Vector Color Red S Line Thickness 3 tat 5 tna Accept Diem EDU fu Re eR EER 7 2 660x108 YANINA sens s AMNEM LLAGAS hs casas aa aaa Gu Ape Ro ME ER e a cl s LL nan 2 60X105 0 5 1015 20 25 30 Meter Figure 23 Vector field tool Displacement field of the 1999 Taiwan Chichi earthquake form a pair of SPOT images 2 Fault Origin Enter the X and Y pixel coordinates of the first point of the fault given by the Cursor Location Value tool If not selected the first pixel found in
75. the GCPS generated A residual misregistration as small as possible is desired Note that if the GCPS were optimized with a Tie Points file the x and y pixel coordinates of the optimized GCPS are minus 1 compared to the initial coordinates COSI Corr is using a pixel coordinates system originating at 0 0 unlike ENVI which starts at 1 1 8 1 Miscellaneous When optimizing GCPS generated from tie points selection between an aerial image and a shaded DEM if the difference in resolution is large example 1 m image vs 30 m SRTM or if the topographic features are too small for a good optimization it is recommended to geolocalized first a satellite image with the shaded DEM and use the subsequent orthorectified satellite image as a reference 9 Orthorectification and Resampling This function will orthorectify an image Aerial Imagery or Satellite Imagery Orthorectification Resampling It is composed of two steps The pixel mapping between the raw image and the futur orthorectified image and the resampling of the image according to the mapping 9 1 Orthorectification 1 image to orthorectify Select the raw image to orthorectify You can define a Spatial Subset i e select a subset of the image that you want to orthorectify You can select also a Spectral Subset i e select the bands of the image you want to orthorectify in case the image is multi band by default all the bands are orthorectified 2 Ancillary d
76. the surface deformation cleared of topographic artefact Please note the following limitations e The epipolar and perpendicular epipolar directions are not know exactly as the acquisition geometries are subject to error and approximation too Consequently the epipolar component will contain most of the topographic residual and some will be contained in the perpendicular epipolar direction e The perpendicular epipolar direction contains the projection of the surface deformation into that di rection The deformation measured in this component is not the absolute deformation but just the projection of it into that direction e This approach only works if the surface deformation in the vertical direction is small compared to the horizontal deformation In the GUI illustrated in Figure 26 enter the following information 1 Master Ancillary Data File Enter the ancillary file of the master image The master image is the one used as the pre event during the correlation In case of frame camera system enter the Exterior Orientation file of the master image 2 GCPS File optional Enter the GCPS file that was used if any to orthorectify the master image 3 DEM optional Enter the DEM that was used if any to orthorectify the master image 4 Slave Ancillary Data File Enter the ancillary file of the slave image The slave image is the one used as the post event during the correlation In case of frame ca
77. tion When done save your tie points selection using File Save GCPs to ASCII and not Save Coefficient to ASCII The file created will be a list of the form x master y master x slave y slave in pixel Note 1 This is an ENVI function that can also be found in Map Registration The ENVI tool accounts for the xstart and ystart contained in the image header Make sure they are set to 1 as COSI Corr assumes so Most likely this will not be the case if your georeferenced master image is a subset of a larger image that has been cropped using ENVI Editing the header of your master image and forcing the xstart and ystart to 1 will not corrupt your data and is mandatory Note 2 If tie points are selected between an orthorectified image and a raw image to be converted to GCPS and optimized here are some guidelines to pick them adequately 7 2 At least three points must be selected If the warp image is to be co registered with a shaded DEM a larger number of points 15 to 30 if possible should be selected to average the probable correlation errors due to the difference in images content Spread the points as much as you can in the image but select them away from the area where surface displacement is expected If displacement is expected in the whole image select points in areas of smallest displacements Do not select points too close to the images borders As the optimization will correlate windows centered on ea
78. two correlators are available frequency Sec 10 1 and statistical Sec 10 2 The frequency correlator is Fourier based and is more accurate than the statistical one It should be use in priority when correlating optical images However this correlator is more sensitive to noise and is therefore recommended for optical images of good quality The statistical correlator maximizes the absolute value of the correlation coefficient and is coarser but more robust than the frequency one Its use is recommended for correlating noisy optical images that provided bad results with the frequency correlator or for correlating images of different content such as an optical image with a shaded DEM 4 Correlation File Select the name of the correlation file to be created 26 If both images are georeferenced with the same projection and resolution the georeferencing is accounted for and only the geographic overlapping part is correlated Otherwise the correlation is pixel based 10 1 Frequency Correlator Si Frequency Correlator Parameters Window Size X Initial 1128 Final 32 Window Size Y Initial 128 Final 32 Step X EN Step Y fie Robustness Iteration 2 B Mask Threshold 0 90 Resampling longer process T Grided Output v OK Cancel Figure 10 Frequency correlator parameters The frequency correlation is a two step process The first step consists in roughly estimating the pixelwise displac
79. ust be georeferenced and can be of any projection If not selected the topography will be considered flat at altitude 0 above the ellipsoid WGS 84 It is strongly recommended to use the same DEM that was used to orthorectify the reference image as DEM errors will then be kept consistent between the two images In case of an optimization with a shaded DEM the DEM used should be the one used to generate the shaded DEM 4 Ancillary IO file Select the ancillary file for satellite or the Interior Orientation file for aerial of the raw image 5 GCPS tie points ICP e GCPS A GCPS file is the most flexible option This is a file Fig 6 whose format is longi tude decimal degree latitude decimal degree altitude meter X pixel Y pixel SNR 0 to 1 OPTI 0 or 1 DX meter DY meter DZ meter and contains at least three GCPS obtained generally from the Tie points to GCPS tool Sec 7 2 22 SNR represents the weight of the GCP between 0 and 1 If the confidence is similar for all points all SNR should be equal and different than zero OPTI is a flag indicating whether the GCP is going to be optimized 1 or not 0 A GCP with the OPTI flag set to 0 will be accounted for during the computing of the EO aerial or Look Angle correction satellite but not optimized A typical example where GCPS should not be optimized would be some GPS points located precisely whereas others GCPS are coarsely estimated Anothe
80. ver 150 unless you have a lot of RAM Windows OS Windows path can be updated from Control Panel System Advanced System Settings gt Environment Variables In the System Variables section clik on New then for the variable name enter IDL_PATH and for the variable value enter pathToCosi lt IDL_DEFAULT gt e g C Users John McClane Documents mySoftware cosi corr lt IDL_DEFAULT gt Note that lt IDL_DEFAULT gt must be typed verbatim Similarly create a new environment variable by clicking on New then for the variable name enter IDL_DLM_PATH and for the variable value enter pathToCosi cosi modules IDL DEFAULT We g C Users John McClane Documents mySoftware cosi corr cosi modules lt IDL_DEFAULT gt Alternatively if you cannot update the environment variables because you don t have the right to admin right needed you can update them using the IDL development environment IDLDE Open ENVI IDL and in the IDL development environment go to Window Preferences IDL click on the arrow next to IDL to diplay menu Paths Then select IDL path in the scrolling menu and click insert Select the pathToCosi directory Click on Move up to place the new path above the IDL_ DEFAULT Select now DLM path in the scrolling menu and click insert Select the path ToCosi cosi modules directory Click on Move up to place the new path above the IDL_DEFAULT You need the Visual C Redistribut
81. ween two displayed vectors Performs the decimation of a displacement field if more than 1 Line Thickness Ratio to determine the thickness of the displayed vectors Note Saving the vector field as an ENVI Layer will not work in ENVI 4 0 due to an internal ENVI error 11 7 Stacking Profiles In the context of seismotectonics this tool Tools Stacking allows to stack profiles across the fault on the correlation file to retrieve the fault step Prior to stacking profiles a mapping of the fault is necessary 1 Using the ENVI ROI tool with the polyline selection option ROI Type gt Polyline map precisely the fault Once the fault is mapped save the ROI using File Output ROIs to ASCII 2 Take note of the fault origin pixel coordinates using the Cursor Location Value tool as it will be needed for the fault orientation 11 7 1 Orient Fault This step Tools Stacking Orient Fault will rearrange the data contained in the fault profile file retrieved from the ROI tool This process is necessary for two reasons First reason practical is the necessity to reorder the fault points to physically follow the fault the ENVI ROI tool save the points line wise The second reason is to define the origin of the fault as it will dictates the fault orientation for measurements made parallel and normal to the fault The parameters are the following 1 Fault Trace ROI Ascii File Select the file genera
82. xels within the search area 11 1 3 Advanced Filter Parameters Fig 13 Minimum weight value Only used if the Linear regression weighting method is selected otherwise it is ignored Only weights above this threshold will be counted in the minimum number of weights computation This sanity check ensures that very small weights are not counted as part of a valid averaging The default value for this field is 0 1 This value must be a floating point between 0 0 1 0 The closer this parameter is to zero the more the linear regression filtering will occur with the risk of fitting the noise for pixels with very few similar patches in the search area The closer this parameter is to one the less the linear regression filtering will occur defaulting to the standard averaging method Minimum of weights Only used if the Linear regression weighting method is selected otherwise it is ignored Minimum number of weighs above the minimum weight value threshold so that the Linear regression filtering can occur Otherwise the filtering method defaults to the averaging filtering method This condition avoids fitting the noise when only very few significant weights exist in the search area This parameter therefore only makes sense if it is larger than three If it is too large linear regression filtering tends to occur less defaulting to the standard averaging method 32 Filter Params Advanced Minimum weight value 0 1

User`s Guide to COSI-CORR Co-registration of Optically Sensed

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