System Administrator`s Manual
Contents
1. P O Box 1080 Blindern 0316 Oslo Norway June 2004 http www mn uio no ifi english research groups dsb resources software xite UsersManual DA 3 H I Christensen and J L Crowley editors XITE X based Image Processing Tools and Envi ronment pages 63 88 World Scientific Singapore 1994 ISBN 981 02 1510 X 2 4 Otto Milvang and Tor L nnestad An image widget for image processing The X Journal 1 2 November December 1991 2 5 Otto Milvang and Tor L nnestad An object oriented image display system In Proceed ings 11th International Conference on Pattern Recognition pages D218 221 The Hague The Netherlands August September 1992 2 16 References 78 79 80 81 82 83 84 85 86 87 88 89 90 REPORTS FROM THE IMAGE PROCESSING LABORATORY Maurycy Szmurlo A comparative study of statistically classifiable features used within the area of Optical Character Recognition Cand Scient Master thesis May 1995 Ingvil Hovig Verkt y og metoder for komprimering av MR bilder Dr Scient Ph D thesis August 1995 yvind Akerhaugen Automatisk plassering av navn pa kart ved hjelp av simulated annealing Cand Scient Master thesis February 1996 Marius Midtvik Reversibel komprimering av MR bilder basert pa statisk kildemodellering Cand Scient Master thesis May 1996 Tor Vyvind Didriksen Linjefinning og klassifikasjon med Random Hough transf2. install xite rpm This completes the installation 2 For non rpm based system e Create an XITE home directory and set the environment variable XITE_HOME to reflect your choice If you need more information about this please refer to ap pendix A 1 e Move the script install xite and the file xite tar gz or xite tar Z or xite tar into the XITE home directory e From the XITE home directory issue the command where represents the shell prompt sh install_xite If you need more information about the install script and how to check for installation errors please refer to appendix A 2 2 1 1 Installing XITE for multiple architectures If you decide to make a complete XITE installation on a different non rpm platform then rerun the script install_xite as explained in section 2 If you simply want to install binary executables object libraries and possibly include files manual pages and hypertext documentation for a platform in the same networked file system while not duplicating the source files and scripts there is no need to unpack XITE again Instead use the command sh install_xite d You may want to check out the p and loc options If you need more information on this please refer to appendix A 3 2 2 On Windows There are two possible ways to install XITE on a Windows host The easiest way is to start from the prebuilt XITE distribution for Windows If your Windows system has access to a UNIX file sy
3. Manual which was built during the installation procedure If firefox is not available xshow will usually try to launch another program The exact behaviour is determined by the X appli cation resources xiteHelper and xiteHelperOption or the environment variables XITE_HELPER and XITE_HELPER_OPTION If you want to customize the behaviour refer to XITE User s Manual 2 or the manual page for xshow Spossibly also XUSERFILESEARCHPATH 8 Customizing the installation 3 5 Customization of the xshow menu tree The main display program xshow can launch most of the other programs supplied with XITE This is done via a menu hierarchy which is defined in an ascii menu file One of the entries in the main menu is Site specific programs If you want all your users to get access to locally developed programs which operate on images in the XITE file format BIFF these programs may appear in a submenu tree below this entry For information on how to add local programs to the menu hierarchy refer to the manual page for xshow 3 6 Compilation of XITE dependent software A script cxite is supplied for compilation and linking of new programs which use XITE routines It was installed in the XITE executable directory you chose during installation On UNIX platforms the script was automatically edited by the install script It should be able to supply the necessary options to find XITE header files the XITE library as well as other required head
4. account for the software Norske emneord Indexing terms Norwegian Engelske emneord Indexing terms English Bildebehandling Image Processing Bildebegrep Image Concept Bildeprogram Display Program Vindussystemet X X Window System Farger Colors UNIX UNIX C C Windows Windows Adresse Address Bildebehandlingslaboratoriet Institutt for informatikk Universitetet i Oslo Boks 1080 Blindern 0316 Oslo epost blabGifi uio no tlf 22 85 24 10 Image Processing Laboratory Department of Informatics University of Oslo P O Box 1080 Blindern N 0316 Oslo NORWAY email blab ifi uio no phone 47 22 85 24 10 XITE X based Image processing Tools and Environment System Administrator s Manual For version 3 48 Image Processing Laboratory Department of Informatics University of Oslo Svein B e September 2013 Contents 1 Introduction 1 1 1 Required disk space vr rv vnr kr ee 1 1 2 Root administrator privileges o o 1 1 3 What you need besides XITE o o e e e o 1 1 4 About this repottiss rias Seg Fee a eke ae 2 2 Installing XITE 3 221 Om UNIX platforms 24 4 2 2 a a ae RA ld ss 3 2 1 1 Installing XITE for multiple architectures o nennen 3 227 Om Windows Lose 20 sama a le a A tt are le Be alg 3 2 2 1 Using the prebuilt distribution for Windows 3 2 2 2 Starting from a UNIX distribution o 4 3 Cust
5. may find more information about XITE in its home page with URL http www mn uio no ifi english research groups dsb resources software xite 10 Miscellaneous 4 6 How to contribute to XITE If any of your users writes software which she would like to contribute to XITE refer her to the Programmer s Manual 1 supplied with the XITE distribution Please email blab ifi uio no if further instructions are needed If anyone at your site makes changes or fixes bugs please let us know Refer to section 4 1 for details on sending a bugreport 11 A Details on the installation procedure If you ran into problems during the UNIX platform installation procedure which was briefly outlined in section 2 you may find help here A 1 XITE home directory For a tarball based installation all the C source code and installation scripts will by default be placed below the XITE home directory For an rpm based installation the source code is packaged inside the source rpm as a tarball The object library executables manual pages and other documentation do not need to reside below the XITE home directory This can be chosen during the installation procedure Set the environment variable XITE_HOME equal to the chosen XITE home directory On a UNIX system if you are using the csh or tcsh shell this can be done with the command S setenv XITE_HOME usr local xite if you chose usr local xite as the XITE home directory If you are using
6. the installation procedure you will be asked whether you want to continue building the library executables and documentation This means that unpacking of the XITE dis tribution has been completed What remains is the actual compilation linking and documentation production This is handled by a separate script makexite which is located in XITE HOME etc If the installation so far has gone by without problems just type y in response to this question and makexite will be started automatically A 2 3 Checking for errors All of the compilation errors and warnings found while the makexite script is run will be stored in a file with filename starting with the string xite_log and with filename extension given by the computer architecture you are installing XITE on You should check this file when the installation is finished looking especially for error messages A quick way of doing this is with a command such as grep i error xite_log IRIX grep v ignored if you are installing XITE on a computer running the IRIX operating system This will tell you whether any errors were found Search through the file to see what the errors were before sending a bug report to the XITE developers see section 4 1 on how to send a bug report A 2 4 Rebuilding of parts which failed If the building of XITE libraries or executables failed you may try to rebuild the system using a different compiler different compiler options or change other informat
7. Image Processing Laboratory Department of Informatics University of Oslo Report No 91 XITE X based Image Processing Tools and Environment System Administrator s Manual For version 3 48 Svein B e September 2013 Bildebehandlingslaboratoriet Institutt for informatikk Universitetet i Oslo Image a Laboratory Department of Informatics University of Oslo Tittel Title XITE System Administrator s Manual Forfatter e Author s Svein B e Rapport nr Report no 91 ISBN 82 7476 061 1 Dato Date September 2013 Resym Abstract XITE consists of display programs with image widget and graphical user interface as well as more than 200 command line programs and 600 sub routines for image processing all documented on line The command line programs and subroutine library are written in C and run under UNIX and Windows The display programs run under UNIX They work with images of arbitrary size and pixel type on 8 bit PseudoColor and 24 bit DirectColor and TrueColor X11 displays Images can be zoomed and panned and colortables can be selected from a menu The main display program xshow gives access to most of the other command line programs via a menu interface which the user can customize and extend to include local programs Input images for the menu entries can be selected with the mouse and output images appear on the display This report describes how to install XITE and how to prepare a user
8. OME lib If you have already started MATLAB the PATH variable can be set from inside MATLAB by setenv PATH getenv PATH getenv XITE_HOME lib In MATLAB add the locations of the mex executables to the MATLAB path The mex executables are spread among a number of subdirectories below XITE_HOME matlab xite if you chose to use the prebuilt distribution You may also need to install C runtime dll as outlined in the previous paragraph concerning the standalone executables 2 2 2 Starting from a UNIX distribution Building standalone executables On a UNIX host run the command sh install_xite d p Win32 This will create makefiles for Windows and the necessary folders for libraries and executables Check the files Makefile Win32 in the directories etc and src to make sure the paths are valid and in Windows notation If Microsoft Visual C 2008 compiler version 9 0 is installed on your system open a Command Prompt window go to the XITE source directory and issue the commands set XITE_HOME full_path_of_XITE_folder C Program Files Microsoft Visual Studio 9 0 VC vcvarsall bat nmake f Makefile Win32 2 2 On Windows 5 Building the XITE to MATLAB bridge The standalone programs for conversion between XITEs biff files and MATLABs mat files biff2matlab and matlab2biff need no special configuration They should have been built by the nmake command above To build the mex files whi
9. an sh compatible shell e g bash use the command S XITE_HOME usr local xite export XITE_HOME Throughout this document the string XITE_HOME represents the chosen XITE home directory Before unpacking building and installing XITE the home directory must be created If you have chosen usr local xite as the XITE home directory issue the commands S cd usr local S mkdir xite You will probably need root privileges to be allowed to create the directory You could of course alternatively have chosen to install XITE below your own home directory in which case you would not need any special privileges at this stage A 2 Unpacking building and installing A 2 1 What you need before unpacking Before you start to build and install XITE make sure that you have everything you need You should have the following files e install_xite e One of xite tar gz xite tar Z xite tar For an rpm based system you only need xite rpm and possibly xite src xpm If you lack any of these files you will find them with a WWW browser pointed to XITE s home page at 12 Details on the installation procedure http www mn uio no ifi english research groups dsb resources software xite Move the above files into XITE_HOME and change to that directory cd XITE_HOME Do not unpack the tar file manually A 2 2 Unpacking the tar ball The script install_xite will unpack build and install XITE To get a list of the various options sup
10. ch can call XITE functions from MATLAB the mex compiler must be configured Run the MATLAB mex script with the setup option to produce a file configured for the chosen compiler mex setup Make a note of where the file mexopts bat is placed and copy it to XITE_HOME src matlab mexopts bat Finally compile all the mex files with the commands 8 cd XITE_HOMEY src matlab nmake f YXITE_HOME etc Makefile Win32 mexobj mexlib xite_mex_dso xitemex mexhelp cd xite nmake f XITE_HOME etc Makefile Win32 mathelp 8 for d d in do cd d amp nmake f XITE_HOME etc Makefile Win32 amp cd 6 Customizing the installation 3 Customizing the installation After having installed XITE successfully there are a few remaining steps which you need to go through manually in order to make XITE operate at its best 3 1 Setup of user accounts 3 1 1 On UNIX platforms The installation procedure also produced setup files for XITE users If you installed the rpm every user logging in to the computer will automatically have the correct setup for XITE Without the XITE rpm the easiest way for a UNIX user to get access to XITE is to invoke XITE setup files from the initialization files of the login shell If the login shell is csh compatible include the following line in the user s cshrc file source XITE HOME etc xite cshrc where XITE HOME is replaced by the actual XITE home directory If the login shell is sh c
11. er files and libraries The command cxite help will give more information about this script cxite is not available under Windows 4 Miscellaneous 4 1 Bug reports If or when you encounter bugs whether during installation or execution please send bug reports to the XITE developers You ll find a bug report template in the file XITE_HOME etc install bugReport or in usr share doc xite 3 48 bugReport for an rpm based installation Mail the bug report to xite bugs ifi uio no 4 2 Registration If you install and use XITE please let us know by filling in the registration form in the file XITE HOME etc install REGISTER or usr share doc xite 3 48 REGISTER Mail it to xite register ifi uio no This will help us get a general idea of what people find useful what platforms XITE is most widely used on and whether the users are in universities research institutions etc The use of XITE is free but we would be happy to know that you find it useful 4 3 Copyright XITE comes with a mild copyright notice You ll find a copy of this in the file XITE HOME etc install COPYRIGHT or usr share doc xite 3 48 COPYRIGHT 4 4 Mailing list An international mailing list exists for discussions about XITE If you would like to subscribe to this list send a mail to xite request ifi uio no The list name is xite ifi uio no 4 5 WWW home page for XITE With your favourite World Wide Web browser such as firefox you
12. formats such as TIFF PNG pnm pbm pgm ppm and MATLAB s MAT files you will need the libtiff TIFF library libpng library Netpbm and MATLAB To build the TIFF to BIFF converters you need an ANSI C compiler such as gcc Inttp www libtiff org 2http www libpng org Shttp netpbm sourceforge net nttp www mathworks com 2 Introduction The XITE display programs need the X Window System Version 11 a PseudoColor 8 plane preferrably or 24 plane DirectColor display It should also work with a TrueColor 24 plane display although the colortables can not be manipulated on such a display Modern workstations often offer all these color modes in a single display 1 4 About this report This report describes how to e install the XITE rpm if this is your preferred installation method e build the object libraries and executables e build hypertext and man page documentation e hook a WWW browser to the Help button in the main display program e prepare user accounts for access to XITE Refer your XITE users to the User s Manual 2 for information on how to use XITE The Pro grammer s Manual 1 describes how to write XITE dependent functions and programs including the use of the X based toolkit ximage ximage is a part of XITE XITE has also been described in 3 4 5 2 Installing XITE 2 1 On UNIX platforms Go through the following three steps in order to install XITE 1 For an rpm based system such as Red Hat
13. ion which was acquired during the unpacking phase Rebuilding of XITE can be done without unpacking the distribution once again Go through the following steps e From the log file try to locate what part of the build process failed In which source directory did it occur Did the compilation of library functions fail or compilation of executables Or perhaps there was an error during the linking phase e Do you think that it would help making changes to the Makefile for the particular archi tecture you are installing on You will find the corresponding makefile in XITE HOME etc with an appropriate filename extension Perhaps you need to change the CFLAGS variable options given to the compiler or perhaps you want to use a different compiler the CC variable e Rebuild the parts of the system which failed by using the script XITE_HOME etc makexite Give the option h to get help on how to use this script 14 Details on the installation procedure A 3 Building XITE on a different platform If you ran into problems when following the instructions in section 2 1 1 read this section If the new platform is unknown to XITE install_xite does not accept the name of your desired platform go through the following steps 1 Edit the script XITE_HOME etc install testPlatform to allow this extra platform 2 Among the platforms mentioned in the testPlatform script decide which one is closer to the new platform Check to see whether the
14. omizing the installation 6 3 1 Setup ot user accounts sr nr a eos a ee baaa 6 3 1 1 On UNIX platforms 2 222 Coon 6 3 1 22 OA Windows 22 tem b Sec eae eis eles 2 hae ee 6 3 2 Building a manual page database o ee 6 3 2 1 On UNIX platforms oo onen 6 3 2 2 On Windows 4 a kag GY ODS STE GE GR Pe ea ee 7 3 3 X app defaults resource files 2 2 Como nennen y 3 4 WWW browser as xshow help program on UNIX platforms 7 3 5 Customization of the xshow menu tree 2 2 CL on nn 8 3 6 Compilation of XITE dependent software 22000 8 4 Miscellaneous 9 4 1 gt BUS TEPOLrts 2 wo ee a Re MA e a as 9 4 2 Registr tion 4a a saga See bb a Ek eh all 9 4 3 Copyrights a 4 aa 23 SOR EE a wo de as ws Sey y as oe BE Oh a as 9 4 4 Mailing lista ii ey oy cee A A SA ul Su ee a e 9 4 5 WWW home page for XITE o e rn rn nen 9 4 6 How to contribute to XITE e 10 A Details on the installation procedure 11 AT XITE Home directory eas a a Era dia ab eo 43 aA g 11 A 2 Unpacking building and installing o nn 11 A 2 1 What you need before unpacking LL o nn nn 11 A 2 2 Unpacking the tar ball o e 12 A223 Checking for errors s sat a ee ae Bi ge al 13 A 2 4 Rebuilding of parts which failed 2 222 m nn o o 13 A 3 Building XITE on a different platform e 14 Refe
15. ompatible e g bash include the following line in the user s profile file XITE HOME etc xite profile As the XITE administrator you should check that the files xite cshrc and xite profile reflect the choices made during installation 3 1 2 On Windows The PATH environment variable must be modified so that XITE programs can be started from the Windows command window Add the name of the folder in which the XITE executable programs reside to this environment variable The folder name is probably bin or bin Win32 below the XITE home directory The environment variable XITE MAN should be set to refer to the folder in which the program manual files reside On a default installation this will be XITE HOME man The environment variable is required for the man and whatis program options to work 3 2 Building a manual page database manual page database is required for the XITE program option whatis to work 3 2 1 On UNIX platforms On a UNIX system the whatis program and man with certain options also need the manual page database The XITE manual pages have been installed in a directory determined by the rpm or which you chose during the unpacking procedure On a UNIX system you should probably go to this Sor XITE HOMEYNman in Windows notation 3 3 X app defaults resource files 7 directory and build a whatis or windex database for the man pages This will enable keyword search with man to work On my local systems I use
16. one of the two commands makewhatis XITE_HOME man catman M XITE_HOME man Replace XITE_HOME by usr share xite for an rpm based installation This may be different on your system 3 2 2 On Windows A windex database and preformatted man pages are supplied with the prebuilt Windows distri bution 3 3 X app defaults resource files This section applies only to platforms with the X Window System installed The XITE display programs will not work properly without the app defaults files If you installed with the rpm they will be located in the standard directory usr share X11 app defaults xite If you installed without the rpm they will be found in the directory XITE_HOME etc app defaults Each display program sets the environment variable XAPPLRESDIR so that the app defaults files can be found by the X Window System If you already have a previous version of XITE it may be that the resource files for the previous version were installed in the standard location You should remove those files A warning will be printed if the display programs can t find these files See documentation on the X Window System for more information about the above environment variables 3 4 WWW browser as xshow help program on UNIX platforms xshow tries to load an external helper application when the Help button in the Control window is pushed The default behaviour is to start the WWW browser firefox pointing to the XITE Refer ence
17. orm en eksperimentell studie Cand Scient Master thesis June 1996 Edward Allen Smith Image Processing Techniques on DNA Fingerprint Images and its Application to Genetic Similarity Analysis Cand Scient Master thesis August 1996 Parviz Heydari Line Following in Digitized Map Cand Scient Master thesis November 1996 Ramin Gordjianfar Vectorization of the Cartographic Data Cand Scient Master thesis November 1996 Luren Yang and Torfinn Taxt Robust Methods for Sonar Bottom Detection February 1997 Christian Wladimir Hansson Strukturgrammatikk en h yeredimensjonal grammatikk for syntaktisk m nstergjenkjenning av 3D objekter i bilder Cand Scient Master thesis December 1996 Sverre H Huseby Video on the World Wide Web Accessing Video from WWW Browsers Cand Scient Master thesis February 1997 Havard Lauritzen Raster til vektor konvertering ved simulert stgrkning Cand Scient Master thesis May 1997 Irene Rodsten Texture Segmnetation using Moment based Features obtained by Locally Adaptive Thresholding Cand Scient Master thesis May 1997
18. ported by this script give the command sh install_xite h Note in particular the options d f and o You may be using these options if you choose to install XITE for multiple computer architectures The easiest way to unpack build and install XITE is to simply issue the command sh install_xite and give the information requested by the script as it runs Be prepared to supply the following e Directory for storage of XITE C header files e Directory for storage of XITE object libraries Directory for storage of XITE executables Directory for storage of XITE manual pages Directory for storage of XITE hypertext documentation The default values suggested by the installation script for the above are all below the XITE home directory For the sake of the display programs in XITE the following information is also needed e Location of header files for the X Window System e Location of object libraries for the X Window System Depending on whether you have MATLAB the libtiff TIFF object library the libpng object library or the Netpbm conversion utilities installed on your system you may also want to supply the location of e libtiff TIFF header files e libtiff TIFF object library e png header files e png object libraries A 2 Unpacking building and installing 13 pnm header files pnm object libraries MATLAB header files e MATLAB object libraries e MATLAB mex files for storage At some point during
19. re is a corresponding Makefile or Makefile template extension tmpl in XITE_HOME etc If you can t find one generate it with the command XITE_HOME etc install makeMakefile p lt platform name gt Make a copy with filename extension equal to the new platform name 3 Incorporate any necessary changes in the Makefile particularly to CFLAGS possibly also to LFLAGS and CC 4 Check the files includes h and xite_ h in the XITE header file directory to see that the appropriate header files will be included with the particular platform You may need to add extra ifdef directives to treat your platform appropriately 5 Use the command sh install_xite d or sh install_xite d p 6 Send an email to blab ifi uio no describing this new platform and any changes or additions you made to XITE in order to make it run References 15 References 1 Svein Boe XITE X based Image Processing Tools and Environment Program mer s Manual for version 3 4 Report 92 Image Processing Laboratory Department of Informatics University of Oslo P O Box 1080 Blindern 0316 Oslo Norway June 1998 http www mn uio no ifi english research groups dsb resources software xite ProgrammersManual 2 10 N Svein B e Tor Lp nnestad and Otto Milvang XITE X based Image Processing Tools and Environment User s Manual for version 3 47 Re port 56 Image Processing Laboratory Department of Informatics Univer sity of Oslo
20. rences 15 iii 1 Introduction XITE pronounced excite is an acronym for X based Image processing Tools and Environment The non display programs run under UNIX System V as well as BSD versions and Windows The display programs are based on the X Window System Version 11 operating in a UNIX environment XITE is at least being used on the following platforms e Windows e Linux XITE consists of C source code documentation some images and colortables and installation scripts If installing from a tar ball the XITE administrator may choose where to locate object libraries executables manual pages and other documentation If instead installing the XITE rpm all locations are predefined 1 1 Required disk space Estimated disk space requirements Source code 10 Mb Manual pages 7 Mb Hypertext doc 3 Mb Other doc 2 25 Mb Scripts images etc 4 Mb Libraries and executables 8 Mb 1 2 Root administrator privileges If you install XITE from the tar ball you may need root administrator privileges for the fol lowing e Creation of XITE home directory e Creation of directories for XITE C header files libraries executables man pages hypertext reference manual and other documentation If you install the rpm you will also need root privileges 1 3 What you need besides XITE If you want to be able to convert images between the XITE file format BIFF Blab Image File Format and other popular
21. stem where XITE is installed e g via Samba you can instead start from this UNIX installation and leave the libraries and executables on the UNIX file system 2 2 1 Using the prebuilt distribution for Windows Standalone executables Go through the following steps 4 Installing XITE 1 Move the file xite zip to the C drive e g C xite or anywhere you choose 2 Unzip the file xite zip This will create a subdirectory xite 3 If the Microsoft Visual C dynamic link runtime library corresponding to your choice of compiler e g msvcr90 d11 is not already installed on your system get the file from the XITE download location or from Microsoft at no cost and copy it to the bin directory which was created when xite zip was unzipped 4 Set the XITE_HOME to refer to the top xite directory e g C xite and set XITE_MAN to refer to the XITE man page directory typically XITE_HOME man The XITE to MATLAB bridge The XITE to MATLAB bridge is a collection of MATLAB mex files which call the XITE programs and return the results as arrays in MATLAB For MATLAB to be able to load and run the mex files MATLAB must be able to find the libraries dlls which the mex files depend on The XITE library DLLs libxite d1l etc must be on the Windows Path or in the same directory as the XITE mex DLLs If the XITE DLLs are located in XITE_HOME lib set the Windows PATH either in the control panel or in a command window with set PATH PATH XITE_H
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