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JARtool User Manual PDF File

1. menu option The user can blink flip the display back and forth between image frames using the Blink accelerator button or the blink option under the Control Panel accelerator button Note Each frame consumes system memory so be careful not to create too many frames This advice is especially relevant when using JARtool features that automatically allocate frames e g the Overlay tool or Production with Auto Display enabled 25 Chapter 5 Labeling The Labeling menu button provides a method for the user to generate training data by circling or otherwise marking objects of interest in the imagery To label an im age simply choose the desired marker shape from the Set Default Marker Shape option in the Labeling menu Note that the interface is always in labeling mode The menu button simply provides control over aspects of the process such as the marker shape and color as well as providing functions to load and save markers Assuming that you have selected the circle marker shape click on the image with the left mouse button drag and release The initial click sets the center of a circle while the drag adjusts the size Releasing the button sets the final size of the circle Markers can be easily moved around resized and deleted Move To move a marker click the left mouse button on or inside the marker and drag to the desired position Resize To resize click the left mouse button on the edge of the marker
2. t exist the FSB will look in a directory defined by the environment variable UPARM for a user directories file In addition to the hot directories defined by the file the list also includes automatically the current working directory CHAPTER 2 JARTOOL BASICS 18 Templates The Templates button is similar to the Hot Directories button By releasing over an item in the template menu the item becomes the current template A template in the Current template entry box can be added to the menu by releasing over the Add template menu option Note that in addition to the predefined templates the list also automatically includes the template which matches any file Programmers Note The file containing the set of predefined templates ap pearing in the menu can be specified through a command line flag tmps when the FSB is invoked If this flag is omitted the FSB checks the current working directory for a file named user templates If that file doesn t exist the FSB will look in a directory defined by the environment variable UPARM for a user templates file Current Selection This entry box holds the user s current selection The selection can consist of a com plete directory pathname and or a partial full filename The current selection can be set and modified in several ways Command Line Argument The initial selection can be specified through a com mand line argument when the FSB is invoked using the flag isel
3. 39 CHAPTER 8 PRODUCTION 40 8 2 Running the Production Software From the Production menu button select the PRODUCTION option This action will bring up a PIG parameter input GUI with the following inputs Inputs control flags These flags allow selected portions of the algorithm to be turned on or off Since the processing is sequential it does not make sense to turn off early stages unless they have been performed in a previous session All flags should normally be set to on this is the default with the possible ex ception of Auto Display and Auto Insert The Links flag creates the out put directory structure and establishes soft links to the image files The FOA flag causes the algorithm to generate candidate locations by applying an FOA filter to the images The SVD Gauss flag causes the algorithm to do fea ture measurement and classification using a Gaussian classifier The Auto Display flag causes the images and corresponding jtri files determined by the production algorithm to be displayed in successive frames at the completion of production For large jobs you will probably want to turn this flag off The Auto Insert flag causes the results of the production run to automatically be inserted into the database If you initially run production with this flag set to off and later decide to insert the results you will need to use the Insert La bels option under the Query Tool Databases menu The production routi
4. The chips can be sorted and annotated based on attributes in the jtri file such as radius label and value Inputs image list This parameter specifies the set of images in VIEW format from which the chips will be extracted The user may simply type the filenames separated by spaces into the entry box Pathnames are required unless the images are in the current working directory The user may also specify a list file using notation Lists can contain a combination of notation and explicit file names The red builder button next to the entry box can be used to construct or specify a list using one of several available methods jtri list This parameter specifies the set of jtri format marker files that indicate where to extract the chips It is criticial that these files exactly correspond with the set of images specified in image list chip size This entry specifies the size of the chips to be extracted chips per row This optional entry specifies how many chips to place on one row in the mosaic If omitted the program tries to make an approximately square mosaic expression This optional entry allows the user to associate a value with each of the chips in the mosaic The value consists of an expression in terms of at tributes defined within the jtri file such as radius label or value The chips in the mosaic can be sorted according to the associated value through the ar range flag The red builder button will dis
5. This threshold specifies how close two points must be to be considered nearby scoring_thr This parameter specifies how close a detection must be to a ground truth location to be counted as correct used to identify not volcano examples for classification training Appendix E Production Parameters To change the behavior of the production algorithm you will need to copy the de fault production_user pars file from jartool analysis defaults and edit the parameters with a text editor such as emacs Cross validation and ruler are no longer supported so be sure to keep xval 0 and ruler no Basically all the parameter values should be the same as you used during the learn ing phase The only parameters that you might want to be different are foa_threshold and gauss_prob_thresh 73 Appendix F Known Bugs in JARtool Busy Box Kill Button There is a potential bug with the busy box kill button When clicked the box does a ps l system command to list currently running processes and then it tracks down all children of the primary process which is to be killed However in the time between performing the ps command and the time when the child processes are actually killed it is possible that new processes could be spawned these will not be killed properly Hot Directories Hot directories added by different users may be placed in the same central file There is no easy mechanism for deleting a hot directory except f
6. This option is only relevant to programmers and users who are calling individual JARtool components from the UNIX command line Typing The user can use the mouse to position the cursor within the entry box and then enter characters from the keyboard The Backspace key deletes char acters behind the cursor while the CTRL d key deletes characters in front of the cursor Special editing features similar to those used in emacs are also available Clicking Clicking the mouse on any item in the list boxes will place that item along with its associated path into the current selection and update the listbox dis play accordingly Hot Directories Releasing the mouse over an item in the hot directories menu will make that item the current selection Tab Completion If the cursor is at the end of the text in the entry area the user may hit the Tab key on the keyboard to complete the current segment of the pathname If there are no matching items or if no additional information is available from Tab Completion the interface will beep If there are multiple matching items the greatest common prefix will be completed CHAPTER 2 JARTOOL BASICS 19 Current Template The current template acts as a filter on all filenames displayed in the list box areas Only filenames that match the form of the template will be displayed To allow up dating when the user types all templates have an implied on the right end Thus the template s will match the f
7. column containing Hometown_ID_Number When we look at the employee records however we do not want to see a Home town _ID_number Instead we want to see the hometown as ordinary text We can achieve this effect by defining a view which is a virtual table derived from the underlying tables The hometown ID numbers would be converted into regular text 28 CHAPTER 6 DATABASE 29 by looking at the second table joining to decode the ID number The lower level tables help the database work efficiently but the views present the information in a more user friendly way In the JARtool database the views will be of primary interest although interaction with the low level tables may also be necessary To provide easy access to the information in the database the Query Tool inter face was designed to be similar in style and layout to the main JARtool interface There are eight components as shown in Figure 6 1 Clockwise from the left we have Accelerator Buttons Menu Bar Results Window Results Buttons Query Window Query Buttons Help Button Accelerator Button Popup Menu DAY UU A LU N 6 1 Accelerator Buttons The buttons along the left side of the display are called accelerator buttons The function of each button in the standard set is described here We use the qualifica tion standard set because the buttons can be re defined by the user Tables list the tables in the active database Vie
8. mv postgres tar gz PostgresHome Change directory to PostgresHome gt pushd PostgresHome Uncompress the postgres tar gz file gt gunzip postgres tar gz This command will produce a postgres tar file Unpack the postgres tar file gt tar xvf postgres tar This will produce a postgresql v6 1 1 subdirectory Change directory to postgresql v6 1 1and follow the instructions in the INSTALL file You must create the directory to hold your data initialize the database and run the postmaster application on some machine which we will refer to as HOST After installing Postgres you must put PostgresHome bin in your path Change directory back to the directory where you downloaded the tar files gt popd 3 Now you can install JARtool on your system as follows a b c d e f g h i G k Create a directory where you would like to install JARtool From here on this will be refered to as JARtoolHome gt mkdir JARtoolHome Move the jartool tar gz file to JA RtoolHome gt mv jartool tar gz JARtool Home Change directory to JARtool Home gt pushd JARtoolHome Uncompress the jartool tar gz file gt gunzip jartool tar gz This command will produce a jartool tar file Unpack the jartool tar file gt tar xvf jartool tar This will produce a jartool subdirectory Change directory to the jartool subdirectory Now compile all the source code gt make PSQL PostgresHome SAOTNG SAO
9. Mean and Standard Deviation 10 3 Image Histogram LL 10 4 Adding New Commands LL Sample Session Sample Session 11 1 Loading an image soanen a a e a e a D a e a e 11 2 saben n io Bo eee A Be e da lo apo iv 28 29 31 34 34 34 34 35 35 36 36 37 39 39 40 42 42 42 44 44 46 47 48 49 51 51 51 51 51 CONTENTS 1 11 9 New Frames 04 18 i aan aa eta n wD as dace 55 114 L ad Markers 533 A da Tel aa ali e a 55 LAS Save Markers ui o aks teeter So eh a ie pi 56 11 6 Learning zi iva SR Ses ey a A 56 1 17 Productions sn pa A SE AO i 57 LS JTREPIMEE 4 pira ee oa e 58 11 9 Chip Mosal rienda ola e e e abs 58 LI LOSCOrino 3c sien sep Le alt aot ee eters aes da 59 1 TDatabas s ca le od ve Pe ok we Ra we Di lee od a 60 Bibliography 65 II Technical Appendices 66 A JARtool Installation 67 B VIEW Format 69 C JTRI Format 70 D Learning Parameters 71 E Production Parameters 73 F Known Bugs in JARtool 74 Part I Reference Manual Chapter 1 Introduction JARtool 2 0 was developed at the Jet Propulsion Laboratory JPL as a prototype system for finding objects of interest in image databases Improvements in acqui sition and storage technology have resulted in image databases that are so large it is no longer feasible to manually examine each collected image Scientists need automated tools if even a fraction of the data is to be analyzed Consider the Magellan mission to Venus Th
10. Substitution define LAT 31 define LON 332 Now click the Execute button This will list all the images which contain the speci fied point on the planet In this case there is only one image in the sample database that contains this point To view this image in JARtool notice that the filename is displayed as a hyperlink blue text Simply click on the hyperlink Listing Labeling Sessions To find out which images have been labeled which person or algorithm did the labeling and the jtri file produced activate the List Records submenu from the Views menu Then select LabeledImages From the Resu ts menu select Display Images and Regions This will display the four images and corresponding jtri files in four different frames If you used the Auto Insert option during the production part of the sample session then there will be a fifth entry pairing the ff20 image with the jtri file generated by production One can also list only the labeling sessions that satisfy a particular criterion Click the JngRgn Auth accelerator button An SQL query will appear in the Query Window Substitute define AUTHORNAME lt AUTHORNAME gt with define AUTHORNAME saleem and click the Execute button All the files that were labeled by saleem should be listed along with the names of the region files he produced Similarly to the image hyperlinks if you click on the name of a region file the region file will be loaded i
11. and drag to the desired size Note that the cursor changes shape when inside a marker or on top of the marker edge Delete To delete a marker hit the delete or backspace key while the cursor is inside or over it There is an undelete option under the Labeling menu Numerical identification labels and text can be attached to any marker Sim ply move the cursor over the marker edge click and hold the right mouse button to bring up a pulldown menu Under the Set Type option there will be prede fined labels that the user can select Simply release the right mouse button over the appropriate label To change a label repeat the procedure the old label will be overwritten Note that these labels are defined in a file that the user can customize 26 CHAPTER 5 LABELING 27 jartool saotng cmds markmap cmds Avoid using the label 0 as this label has a special meaning to some of the JARtool programs In addition it is possible to attach more general text such as Best volcano I have ever seen To do this release the right mouse button over the Attach Edit Text option This will bring up an entry box into which you can type text Multi line text is allowed Click the OK button when finished To save the markers to a file select the Save Markers option under the La beling menu button There is also an option to load markers from file Note that markers are saved in a file format called JTRI which is a JARtool exten
12. and production operations as well as some of the tools only work with VIEW format There is a format conversion operation under the Jools menu bar button that can be used to convert a number of formats such as FITS RAS PDS and VICAR into the JARtool VIEW format Details of the VIEW format are covered in Appendix B Two parameters in the start up configuartion file control the maximum size im age that can be loaded at full resolution Larger images will automatically be block averaged to reduce the size Do not set these parameters to be too large however as you will quickly consume all of your system s memory The default values are XIMTOOL_FRAME_WIDTH 1280 XIMTOOL_FRAME HEIGHT 1280 Note that there is no support for true color images Indexed color images in which each pixel is an index into a color table are not supported either unless the 23 CHAPTER 3 IMAGES color table happens to be one of the default tables provided by SAOtng 24 Chapter 4 Frames A frame is simply a buffer containing an image Multiple frames may exist at one time but only one of these is mapped to the image display area at a time The Frames menu button provides options for creating new frames and selecting which frame will be displayed in the image area As an example the user may load an image into frame 1 create a new frame frame 2 and load a new image there The user may then go back to the first image by selecting the Go to Frame 1
13. appear in the box indicating where it is expecting your input Entry boxes typically have the following keyboard bindings CTRL a Move the insertion cursor to the beginning of the box CTRL e Move the insertion cursor to the end of the box CTRL k Delete the text from the insertion cursor to the end of the box BACKSPACE Delete the character behind the insertion cursor DELETE Same as backspace Both of these keys will also delete selected high lighted text CTRL d Delete the character in front of the insertion cursor CTRL f Move the insertion cursor forward one character CTRL b Move the insertion cursor backward one character TAB In entry boxes that expect a filename or lists of filenames the tab key pro vides filename completion In other words you can type the first part of the filename hit tab and the system will automatically try to complete the file name In addition entry boxes have the following mouse bindings Clicking the left mouse button will place the insertion cursor at the position of the mouse click Dragging the left mouse button will select highlight text Dragging the middle mouse button will scan or scroll text that is too long to fit within the entry box CHAPTER 2 JARTOOL BASICS 16 2 15 Builder Buttons Several parameter inputs GUI s PIGs contain a red button next to some of the pa rameters These buttons provide an alternative means for entering parameter values as opposed
14. dialog box will verify the request before destroying the image There is a bug in the SAOtng system that causes the menu options under the menu bar buttons to disappear when an image is destroyed The options can be restored by loading a new image into the display See Appendix F for a list of known CHAPTER 2 JARTOOL BASICS 9 bugs Load Markers This button provides an interface for loading a JTRI format marker file onto the current display Click and release the left mouse button to bring up a dialog box You can then directly type the jtri filename into the pink en try box or click on the red builder button to the left of the entry box to invoke a file browser The new markers are merged with existing markers If desired use the De stroy Markers command before loading to clear pre existing markers Save Markers This button provides an interface for saving the currently displayed markers to a JTRI format file Click and release the left mouse button to bring up a dialog box You can then directly type the save filename into the pink en try box or click on the red builder button to the left of the entry box to invoke a file browser Destroy Markers This button provides a shortcut for destroying all of the cur rently displayed markers A popup dialog box will verify the request before destroying the markers To delete individual markers move the cursor inside or over the marker and hit the delete or backspace key on the keyboa
15. hold the left mouse button to see the options The Set Zoom Factor option sets the zoom to a predetermined value 1 2 or 4 A zoom factor of 1 is the normal display setting when an image is loaded A zoom factor of 2 will blow up the central displayed area to fill the entire display Use the panner to set the zoom center by adjusting the image so that the desired zoom center appears at the center of the display The Current Zoom x Factor option zooms in factor gt 1 or zooms out factor lt 1 The difference between this option and the Set Zoom Factor is that here the resulting zoom is relative to the current zoom setting rather than an absolute number Neither the Set Zoom Factor nor Current Zoom x Factor affect the func tion of the Zoom In or Zoom Out accelerator buttons which are hard wired to multiply the current zoom by 2 and 1 2 respectively Following a long sequence of pans and zooms the option Reset and Recen ter Zoom can be used to go back to the original view like when the image was first loaded This button provides a menu of image flipping options Click and hold the left mouse button to see the options they are all self explanatory Note that a flip operation can be undone by applying the same flip operation a second time Pan Mag This button provides control over the panner magnifier The user can choose between panner magnifier and no display The user can also c
16. image rows and columns The jtri files do not include information about the im age size In order to implement the border exclusion feature the program must request this information from the user Outputs The output is a popup box that shows the confusion matrix entries The user can save these to file by clicking on the Save button Currently only an ascii save format is supported Sq showmat src E A A POE AE E TTT TTT 130 22 30 36 33 243R ss ile SA le Save i Quit L al Figure 9 3 Confusion results 9 6 Overlay The Overlay Tool allows the user to display in successive frames a list of images overlaid with the corresponding jtri file For the lists the user may simply type the filenames separated by spaces into the entry box Pathnames are required unless the images are in the current working directory The user may also specify a list file using notation Lists can contain a combination of notation and explicit filenames The red builder button next to the entry box can be used to construct or select a list using one of several available methods The jtri list may be omitted CHAPTER 9 TOOLS 48 New frames are created for each image Results are displayed in the new frames Be careful when using this feature not to create too many frames because each frame consumes memory 9 7 Chip Mosaic The Chip Mosaic tool enables the user to extract chips regions from a list of im ages and display these in a mosaic
17. trai ira ie era dn 13 2 9 Colorbar Popup Menu oaaae 13 2 10 Text Information LL 13 2 11 Help Button iene e ee ead tia 13 2 12 Marker Popup Menu LL 13 2 13 Parameter Input GUI s PIG s LL 14 2 14 Entry BOXES i pi Goel hee e a 15 2 15 Builder Buttons 2 0 2 ee ee 16 2 16 File Browser File Selection Box FSB 16 ZA Last Files ta da deal es eh A 20 2 18 Busy BOXES ii i A ai de e 20 2 19 Marker Analysis Tasks o o 21 3 Images 23 4 Frames 25 5 Labeling 26 lil CONTENTS 6 10 I 11 Database 6 1 Accelerator Buttons 20 6 27 Ment Bate apa peli ee lea gn 6 3 Results Window LL 64 Results Buttons 000000 A dd gi 6 5 Query Window e 6 65 Query Buttons l s ao e Paola aa 6 7 Help BUON cpu iii Pa La eee ee Be pe 6 8 Accelerator Button Popup Menu LL Learning 7 1 Algorithm Overview o 0000000004 7 2 Running the Learning Software Production 8 1 Algorithm Overview e e 8 2 Running the Production Software Tools OA XEIstEditor iodio 92 EistExpression soci a gee GALA Aa are see eo ea 9 3 Format Conversion e 0000000004 94 JERFPIEr e A AAA A 9 0 CONTUSION sorteo tel a bee Pte aes e dos Bele tea 96 Overlay doi a ee ee doe dr 9 1 Chip Mosalc siva Mai ii DA ai ect 98 FEhumbnall api bow a a User Commands 10 1 Image Min and Max ouaaa aaa 10 2 Image
18. IRCLE 352 438 16 639999 2 1 2 This entry specifies a circle centered at 352 438 with radius 16 64 pixels The 2 and 2 indicate the color and label scientist s confidence of this object The label may also be followed by another field indicating time or other attribute as well as a text comment preceded by Multi line comments are possible by using backslash n to represent line breaks 70 Appendix D Learning Parameters To change the behavior of the learning algorithm you will need to copy the de fault learning_user pars file from jartool analysis defaults and edit the parameters with a text editor such as emacs Cross validation and Ruler are no longer supported so be sure to keep xval 0 and ruler no We recommend experimenting only with the following parameter values fullresize The size of the images at full resolution This parameter is used to scale the coordinates of objects detected on reduced size versions of the im age back to the full size coordinates foa_threshold This threshold determines how aggressively the focus of attention will be in declaring things to be candidate volcanoes Lowering the thresh old will make the FOA more aggressive raising the threshold will make the FOA more conservative If the threshold is too low too many things will be detected while if the threshold is too high no objects will be detected so it may be necessary to experiment to find an appropriate v
19. JARtool 2 0 JPL ADAPTIVE RECOGNITION TOOL USER S MANUAL Developed by M C Burl S Mukhtar J C Roden M P Burl P Smyth U M Fayyad Machine Learning Systems Group Information and Computing Technologies Research Section Jet Propulsion Laboratory California Institute of Technology September 16 1997 Copyright 1997 California Institute of Technology ALL RIGHTS RESERVED U S Government Sponsorship Acknowledged NAS7 1260 JPL NASA il This document describes a system that was developed at the Jet Propulsion Laboratory California Institute of Technology to provide scientists with tools to analyze large image databases No representations are made about the suitability of this software for any purpose It is distributed as is without express or implied warranty and without technical support For further information contact Dr Michael C Burl 818 306 6422 burl aig jpl nasa gov Copyright 1993 1997 California Institute of Technology ALL RIGHTS RESERVED U S Government Sponsorship Acknowledged NAS7 1260 Typeset with I amp TEX Contents I Reference Manual 2 1 Introduction 3 2 JARtool Basics 6 2 1 Accelerator Buttons LL 7 2 27 MENU Bare ae A ei 11 2 3 Panner Magnifier e 0000000004 11 2 4 Panner Magnifier Popup Menu 12 2 5 Image Display Area LL 12 2 6 Coordinate Display oaa 12 2 7 Coordinate Display Popup Menu 12 23 Colorbar
20. PTER 1 INTRODUCTION 4 lem of visual detection of localized objects occurs in many domains including mili tary surveillance medical image anlysis etc With hand coded features a new sys tem would need to be developed for each new problem domain Given these limitations we elected to pursue a learning from examples approach in which the geologists domain knowledge was captured not through explicit rules but through examples of the objects of interest This in fact is the fundamental idea behind JARtool A scientist or other user provides a set of training examples by using the graphical user interface GUI to label target objects within a set of im ages During a learning phase the system uses these examples to build an appear ance model of the object During a production phase the learned model is applied to other images to find novel instances of the object Although JARtool was developed in the context of locating small volcanoes in the Magellan dataset the fact that it is trainable in principle means that the system can be applied to other datasets merely by supplying the appropriate training exam ples However in practice this is not quite the case The system uses as examples fixed size regions centered on the object Thus if an object class exhibits large vari ations in scale the JARtool approach will not work well For the volcano problem we were fortunate the volcanoes do vary significantly in scale but a fixed size
21. Training examples are specified to the sys tem by giving a list of images and the corresponding list of jtri files Each jtri file contains markers circles that indicate the location of objects of interest Inputs control flags These flags allow selected portions of the learning algorithm to be turned on or off However since the processing is sequential it does not make sense to turn off early stages unless they were performed during a previous session All flags should normally be set to on this is the default The Links flag creates the learning output directory structure and establishes soft links to the images and label files The FOA flag causes the algorithm to learn an FOA filter and apply the result to the training images with scoring The SVD Gauss flag causes the algorithm to do feature learning and classification using singular value decomposition SVD and a Gaussian classifier image list This parameter specifies the set of images in VIEW format to be used for training The user may simply type the filenames separated by spaces into the entry box Pathnames are required unless the images are in the cur rent working directory The user may also specify a list file using notation Lists may contain a combination of notation and explicit filenames The red builder button next to the entry can be used to construct a list using a graphical interface or to look for a specific list that was previously stored in a fil
22. Views menu list records in Objects This will list the position of all vol canos in the database To do a more interesting query click Obj Img Edit the query by substituting define IMAGENAME lt IMAGENAME gt with define IMAGENAME jartool data images ff05 sdt Click Execute query to list all the volcanos in the database contained in this image Now click Display Regions and the listed volcanos will be drawn as points Note that the Obj Img and other Obj queries are not applying any of the de tection recognition algorithms to the image They are only conulting the database to see if someone or some algorithm has recorded labels on the designated image CHAPTER 11 SAMPLE SESSION 63 Also the objects may not actually correspond to true volcanoes e g an algorithm may have generated false alarms which were then inserted into the database Acknowledgements The authors wish to thank the developers of SAOtng at the Smithsonian Astophysics Observatory for their responsiveness to our requests for improvements and new fea tures We also thank Jayne Aubele and Larry Crumpler our planetary geologist col laborators Jayne and Larry evaluated early versoins of the system and provided valuable feedback that helped guide the development of the version 2 0 system In addition we wish to acknowledge the following people who were involved either in earlier versions of the JARtool interface or in algorithm development and testing La
23. YPOS 4 5 Be s sia O ORIENT ala SR EA I sn asin C COLOR V VALUE 0 e t m alan atan a a o 3 gt 3 2 PA S Lele Figure 9 2 PIG for the JTRI filter tool The expression builder button brings up two calculator style menus that can be used to specify a filter expression Hints e The filename sao has a special meaning In particular it refers to the cur rent display Thus if sao is specified as the input the currently displayed CHAPTER 9 TOOLS 46 markers will be filtered Similarly if sao is specified as the output the fil tered markers will be drawn on the current display old markers will first be deleted e The JTRI filter tool can be used to copy a list of jtri files to a new set of names by specifying the filter expression 1 e The JTRI filter tool can also be used to filter the output of production so that only those regions identified as instances of the target object are actually dis played In other words regions identified by the FOA but rejected by the clas sifier are not displayed To acheive this effect use the filter expression L 1 9 5 Confusion The Confusion tool enables the user to compare two sets of jtri files and calculate confusion matrices This feature is useful both for comparing the consistency of one labeler versus another and for comparing algorithms against ground truth Inputs jtri list d
24. alue A good rule of thumb is that the FOA threshold should be adjusted so that 80 95 of the true objects are detected patchsize This parameter specifies how large a patch around each object to ex tract and give to the learning algorithm The patch must be large enough to contain a distinctive pattern spoilfactor As a computational speed up much of the processing is done on re duced resolution block averaged images This parameter specifies the block size 71 APPENDIX D LEARNING PARAMETERS 72 spoilpatchsize This parameter is just the ratio of the patchsize and spoilfactor The program should be able to compute this value but due to a bug you must do the calculation yourself and enter the proper value lIbl ulbl These parameters specify the lowest and highest labels in the ground truth jtri files default 1 4 gauss_prob_thresh This threshold specifies how aggressive the classifier is in declaring candidate regions to be volcanoes At low thresholds the classifier is very aggressive at high thresholds the classifier is conservative border_thr This parameter excludes a border around the images The filtering and feature measurement operations use templates that may extend off the edge of an image The resulting values are often abnormal and should be ex cluded The parameter value should be set to half the patchsize cluster_thr Nearby detections are grouped and attributed to the same object
25. area near the center is distinctive enough to support reliable detection Analagous to the limited variation in scale assumption the system works best if there is also lim ited variation in object orientation and illumination direction but may work even if these conditions are not satisfied A recent improvement to the system was the addition of the Postgres database which is used to maintain labeling results and meta data about image sets Scien tists can interact with the database using both pre canned and ad hoc SQL queries The database adds a new dimension to the system as scientists can now formulate complex queries such as show me the number of volcanoes detected by the system in this area of the planet Further the database query tool contains specialized vi sualization features that connect the results of a query back to the JARtool display Incidentally JARtool is built on top of a public domain image display package and graphical user interface developed by the Smithsonian Astronomical Observatory SAOtng v1 7 The manual is organized into three main parts I Reference Manual the part you are reading now ID Sample Session and IID Technical Appendices Each of the parts contains one or more chapters Chapter 2 covers the basics of the JARtool user interface including the physical layout of components and their functionality Chapters 3 10 cover each of the JARtool menu bar functions in more detail Chap t
26. beled the specified object Quit exit from the Query Tool To activate a particular accelerator button simply position the cursor over the button and click the left mouse button Except for the Quit function clicking the left mouse button over an accelerator button will cause one of the following actions e If no additional information is needed from the user the query will be per formed and the results displayed in the Results Window e If additional information is needed from the user the SQL query will be dis played in the Query Window The user can then enter the required parameter values for example a latitude and longitude by editing the arguments of the define statements at the top of the query and then execute the query 6 2 Menu Bar The menu bar consists of the buttons near the top of the display Clicking the left mouse button on a menu bar item causes a pulldown menu to be displayed To se lect an option from the pulldown menu move the mouse over the option and click the left mouse button An option can alternatively be selected by dragging and re leasing the left mouse button Databases This menu contains the following options Connect to connect to a database server Insert Labels insert labeling records into the database You will be asked to pro vide the name of a file The file will contain a number of lines and each line will have an image filename a jtri filename and an author name separa
27. e jtri list This parameter specifies the set of ground truth files in JTRI format to be used for training It is important that these files exactly correspond with the set of images specified in image list user parameter file This entry should be the name of a file that sets up various user defined parameters that affect the learning process e g the size of the ROT s the threshold applied to the FOA output etc The user can modify the parameters by copying the default file and changing it with a text editor such CHAPTER 7 LEARNING 38 as emacs Changing this file is only recommended for experienced users Re fer to Appendix D for more information output directory This entry specifies the root directory that will contain the re sults of learning i e the learned models The directory and its subdirectory structure will be created if it does not already exist If the directory and sub directory structure already exist the contents may be overwritten Outputs The primary outputs of learning are the filter to be used for the FOA algorithm the set of templates principal components to be used to extract features and the statis tics used by the classifier to map from feature vectors to class labels The outputs are organized into several subdirectories images labels pars FOA and CLASS The images and labels directories contain symbolic links to the actual images and labels The pars directory saves all the us
28. e objective of this mission was to provide global mapping of the planet s surface The mission was highly successful achieving 98 coverage and returning more data than all previous planetary mis sions combined Planetary geologists were understandably excited about the possi bilities opened up by this new dataset but they were also overwhelmed by the sheer volume of data One area of particular scientific interest on Venus is volcanism which is the dominant geological process on the planet Geologists predict based on previous low resolution data that approximately one million small volcanoes are visible in the Magellan dataset However to manually catalog all of these would require an estimated ten to twenty man years The JARtool project was initiated to investi gate automating the cataloging process through the use of pattern recognition and machine learning techniques The standard approach to a problem of this type would have been to develop hand coded volcano specific detectors based on rules provided by the domain ex perts the planetary geologists However there are several drawbacks to this ap proach 1 geologists can readily identify examples of volcanoes but they have difficulty verbalizing which characteristics of the image led to their decision 2 even when expert rules are available e g volcanoes have a circular planimetric outline they are not easily translated into pixel level constraints and 3 the prob CHA
29. eling Under the Tools menu select Confusion This action will bring up the Confusion Parameters PIG You will need to make the following changes e Change the first jtri list parameter detections to your_home JAR_markers jtri no sign CHAPTER 11 SAMPLE SESSION 60 e Change the label limits to 1 1 e Change the second jtri list ground truth to jar_home data labels ff20_consensus jtri again no E sign e The label limits in this case should be 1 4 After making these changes click on the OK button In a few seconds a gray window will popup showing the confusion matrix The i j entry is interpreted as the number of objects labeled i by the system and labeled j by the consensus The 2 j entries represent objects not identified by the system but identified by the con sensus of scientists misses The 1 5 entry corresponds to objects identified by the system but not by the scientists false alarms Keep in mind that for the Magellan data the ground truth labels are subjec tive In other words different scientists will not identify exactly the same set of ob Jects as volcanoes Hence in evaluating the system performance we must compare how well the system agrees with ground truth to how well an individual scientist agrees with ground truth As an exercise calculate the confusion matrix between your labels and the ground truth How did you do compared to the JARtool s
30. elow will display the contents of directories You can single click on any of these to navigate through the directory structure Eventually you will get to your home directory Go to the Hot Directories menu button within the file browser and select Add Current Directory This will enable you to quickly go to this directory again in the future Notice that your directory is now added as an option under the Hot Directories menu Finish typing the filename you want for your file say ff20_mylabels jtri When you are done click on the OK button 11 6 Learning Now let s try out the JARtool learning function Click on the Learning menu button and release on the LEARNING menu option This action will bring up a param eter input GUI PIG titled Learning Parameters Click on the red builder button next to image list and select XlistEditor Un der the File menu button select Load File List This action will bring up a JAR tool dialog box Click the OK button to accept the default entry The files from this list will will now appear in the XListEditor under Current List Adjust the scroll bar beneath Current List so that you can see the filenames Double click on ff20 sdt to remove this item from the current list Again go under the File menu button but this time select Save File List Use the red builder button to invoke the file browser Under Hot Directories select your home diredctory Type the filename
31. er 11 presents a detailed sample session that the user can follow to get a quick feel for the capabilities of JARtool Finally the technical appendices include chapters CHAPTER 1 INTRODUCTION 5 on installing JARtool the VIEW image format the JTRI marker file format learn ing parameters production parameters and a list of known bugs Much of the reference information contained in this manual is also available in hypertext form through the JARtool Help button In addition the hypertext doc umentation contains a list of frequently asked questions and answers FAQ The FAQ is not included in the hard copy manual Chapter 2 JARtool Basics To get started with JARtool we recommend that you first study the information here and then jump ahead to the sample session described in Chapter 11 Note We as sume you have already successfully installed JARtool on your system If not see the instructions in Appendix A After trying the examples in the sample session return to Chapters 3 10 for more detail on any of the system capabilities The JARtool interface consists of twelve components which are physically laid out as in Figure 2 1 Clockwise beginning from the left we have Accelerator Buttons Menu Bar Panner Magnifier Panner Magnifier Popup Menu Image Display Area Coordinate Display Coordinate Display Popup Menu Colorbar OMAN AN DI WN Colorbar Popup Menu Text Information Help Butto
32. er and system pa rameters used during the learning process The FOA directory contains the matched filter as well as its performance assess ment on the training set If you are experimenting with the system on a new data set you may want to look at the sc files to evaluate whether the FOA threshold you are using is reasonable The first two entries in the sc files are the number of false alarms and the number of true detections respectively assuming all label categories are treated as object The next n entries are the number of detections in each label category where n is the number of label categories The last n entries are the number of ground truth objects in each label category From these numbers you can get a rough idea of how the FOA is performing at the selected threshold Keep in mind that the FOA is designed to be aggressive low miss rate but poten tially high false alarm rate See Appendix D for more information on how to set the FOA threshold The CLASS directory contains several subdirectories corresponding to differ ent numbers of features The subdirectory with the largest number of components contains the templates principal components used to extract features Each of the _components subdirectories contains classifier statistics for the specified num ber of features Chapter 8 Production The Production menu button provides access to the JARtool production capability which is used to apply an appearance
33. etections This parameter specifies one set of jtri files If the two sets of jtri files correspond to detections and ground truth then this first list should be the detections The user may simply type the filenames separated by spaces into the entry box Pathnames are required unless the images are in the current working directory The user may also specify a list file using notation Lists can contain a combination of notation and explicit file names The red builder button next to the entry can be used to construct or select a list using one of several available methods label limits detections This input consists of two parameters specifying the lower and upper limits of labels that can appear in the detection jtri files jtri list ground truth This parameter specifies the second set of jtri files If one set of the jtri files corresponds to ground truth it should be specified here label limits ground truth This input consists of two parameters specifying the lower and upper limits of labels that can appear in the ground truth jtri files scoring distance threshold A detection and ground truth entry are matched up if they are within this distance from each other border exclusion threshold Detections and ground truth entries that are closer to the image border than this threshold will be discarded and not used in com putation of the confusion matrix CHAPTER 9 TOOLS 47
34. f the image You can see the entire image within the display area by clicking on the Zoom out accelerator button 11 2 Labeling Try out the labeling capability The current marker shape appears under the Label ing menu button The initial default is a circle Change the marker shape to a rect angle by clicking on the Labeling menu button and dragging to Set Default Marker Shape This action will bring up a submenu called Select Marker Shape Drag over and select Rectangle by releasing the mouse button Now try to draw rectangles around all the volcanoes that you can find in the ff20 image To draw arectangle click with the left mouse button to set one corner drag and release to set the other corner For each of the rectangles you draw indi cate your confidence that the object is actually a volcano by clicking the right mouse button on the edge of the rectangle and pulling down to the Set Type option This action will bring up a submenu titled Set this Marker s Type and color Choose the appropriate confidence level and release Continue until you have labeled all the objects you think are volcanoes 11 3 New Frame Generate a new frame by clicking on the New Frame accelerator button Select load image again and load the default ff20 image into this frame 11 4 Load Markers Click on the load markers accelerator button This will bring up a JARtool dialog box with the default jtri marker filename jarto
35. formation 2 12 Marker Popup Menu In order to activate this popup menu position the cursor inside a marker now re ferred to as the active marker Hold down the right mouse button To select an option drag the mouse until the desired option is highlighted and then release the mouse button The available options enable the user to change the color label and CHAPTER 2 JARTOOL BASICS 14 shape as well as to associate text with a marker The user can also perform some local operations on the part of the image which lies inside the marker The available operations are present under the Marker Analysis Tasks menu which is discussed later in this chapter 2 13 Parameter Input GUI s PIG s Virtually every JARtool function requires some parameters to be input by the user These parameters are collected using a set of special purpose parameter input GUP s or PIG for short A typical PIG may contain entry boxes radio buttons checkbut tons sliders or other data entry widgets Figure 2 2 shows the PIG used with the JARtool production process Production Parameters nl control flags LES FOA j SVD GAUSS W AUTO DISPLAY proj mgn sar2 jartool data images ilisy Y output directory proj ngn sar2 jartool data production Ok Cancel Help L al Figure 2 2 The parameter input GUI PIG for the JARtool production process After specifying all the required parameters to the data entry widgets cl
36. g the Toggle Marker Text option under the Labeling menu button 11 10 Scoring Let s see how well the JARtool system labels compare with those of the scientists First we will just blink the display between frames 2 and 3 The Blink Frames ac celerator button will cycle through frames 1 2 and 3 so we will need to use the Control Panel accelerator button to set up a different blink protocol On the Control Panel there is an area labeled Blink with frames set to 1 2 3 Clicking on each of the small grey boxes will increment through the frame numbers similar to setting a digital alarm clock Change the frames to 2 3 and then click the Blink Frames box You can change the blink rate using the arrow buttons An alternative way to visualize the results is to load the scientists markers into the same frame as the JARtool system markers Go to frame 3 and click the Load Markers accelerator button The default filename should be correct so just click OK The scientists markers appear as circles while the JARtool system markers appear as squares Objects marked with both a circle and a square were identified as volcanoes by both the scientists subject to the confidence statement and the sys tem Circles with squares are misses by the system and squares without circles are false alarms We can quantify how well the system works by computing a confusion matrix between the system and the scientists consensus lab
37. he Query Window Prev Query display the previous query in the Query Window Next Query display the next query in the Query Window Add Query add the currently displayed query to the set of accelerator buttons Remove Query remove an accelerator button Execute Query execute the query displayed in the Query Window Execute Queries from File execute queries stored in a text file CHAPTER 6 DATABASE 33 Results Menu This menu contains the following options Clear Results clear the results window Save Results as text file save the results as a text file Display Images and Regions if ImageName and RegionName are among the dis played attributes selecting this option will display in successive frames each image with the corresponding region file overlaid Images Menu This menu contains the following options Display Images if the displayed results contain ImageNames this option will display the images in successive frames Display Thumbnails if the displayed results contain ImageNames this option will display a single image of thumbnails which are reduced size versions of the original images Save Results as image list if the displayed results contain ImageNames this option will produce a text file containing the image filenames This feature is useful since the learning and production routines operate on lists of image files Regions Menu This menu contains the following
38. hods thumbnail size This entry specifies the size of each thumbnail in absolute pixel units For example 64 64 means that each image should be resized to 64 pix els by 64 pixels spoil size This entry specifies the size of each thumbnail relative to the original size of the corresponding image For example 8 8 means that each original image should be reduced by a factor of 8 in each dimension Exactly one of the inputs thumbnail size or spoil size must be provided by the user images per row This optional entry specifies how many thumbnails to place on one row in the mosaic If omitted the program tries to make an approximately square mosaic Outputs The output is a mosaic image that will be displayed in the current frame CHAPTER 9 TOOLS 50 I r Mosaic Parameters proj ngn sar jartool data inages f20 sde proj hqn 3ard 5artool data LabeL 20_consensus jtri chip size 5050 chips per xov expression L a arrange y natural y descending ascending a b Figure 9 4 a Sample parameter values for the chip mosaic tool b Result of run ning chip mosaic with the given parameters Chapter 10 User Commands The User Cmds menu contains some simple image processing functions The user can extend the functionality of JARtool by adding their own routines to this menu 10 1 Image Min and Max This function computes the minimum and maximum data values o
39. ick the OK button to begin processing If you instead change your mind and decide you don t want to do a function just click on the Cancel button Most PIG s come with hypertext help files which can be accessed through the PIG s Help button Another feature that is common to many PIG s is a builder button which ap pears as a red ball at the left of certain parameter input widgets The builder buttons CHAPTER 2 JARTOOL BASICS 15 provide the user with an alternative means for entering parameters instead of just typing in the values Some parameters are optional These are designated by square brackets around the parameter name For most PIG s the OK button will be disabled until all of the required parameters have been specified by the user A nice feature of the PIG s is that they have memory If you invoke the same function more than once the PIG will initialize the parameters to the last set of values used with the function The PIG s have factory default values that are used initially but the user can customize these for their own system 2 14 Entry Boxes Many of the parameter input GUI s PIGS and the JARtool dialog boxes have entry boxes pink rectangular areas for entering text Provided that an entry box has focus the user can simply type on the keyboard and the text will appear in the box To give a particular box focus just click in the box with the left mouse button You will see the insertion cursor
40. iles cat s dog s as well as cat sdt dog spr etc The template acts only on files not on directories The template matches with any file Setting the current template can be done through a command line flag itmp at startup by typing in the entry area or by using the Templates menu Note that because most templates contain the special asterisk character you must enclose the template in double quotes if using the command line option e g itmp sdt One word of caution since only files that match the template are displayed in the listboxes it may seem that some of your files are missing Of course this is only in the listbox display your files are still on disk Changing the template to will enable you to see them again List Boxes The three list boxes are the guts of the FSB These show the hierarchical directory structure associated with the Current Selection The label at the top of each list box shows the directory whose contents are displayed in the list box For example in Figure 2 3 the middle list box has the label data hence the items appearing in this list box are the contents of the directory proj mgn sar2 jartool data The item refers to the parent directory Since images is highlighted in the middle list box the contents of this subdirectory of data are displayed in the right list box Ok Clicking the mouse on the Ok button will cause the FSB to termina
41. isplay Thumbnails ifa set of image names is displayed in the Results Window this button will display a thumbnail image containing reduced size versions of all the images 6 5 Query Window This window can be used to enter SQL queries We do not attempt to explain the SQL language but there are many books available on the topic You can learn some of the basic syntax by examining the pre canned queries which are mapped onto the accelerator buttons To enter an SQL query position the mouse over the Query Window and click the left or middle mouse button to give the window focus Then simply type in your query To execute the query click the Execute button or select Execute Query from the Query menu 6 6 Query Buttons This part of the interface contains some query related buttons The buttons and the functions they perform are as follows Execute execute the query displayed in the Query Window Clear Query clear the Query Window CHAPTER 6 DATABASE 35 Prev Query display the previous query in the Query Window Next Query display the next query in the Query Window Add Query add the query displayed in the Query Window to the Accelerator Buttons 6 7 Help Button At the lower left of the display is a Help button that provides access to the hypertext documentation Click the left mouse button on any highlighted words to get more information 6 8 Accelerator Button Popup Menu The accelerator button p
42. ith JARtool and how to do it 11 1 Loading an image Click on the load image accelerator button This will bring up a JARtool dialog box with the default image name jartool data images ff20 sdt Here and throughout the sample session jartool will be a placeholder for the directory in which the JARtool system is installed typically something like usr local JARtool Click the OK button of the dialog box and the image will be loaded Notice that the text information area at the bottom of the JARtool interface now contains the name of the displayed image as well as the size dim 1024 1024 and blocking factor bl 1 Two parameters in the JARtool config file specify the largest image size default 1280 x 1280 that can be loaded without blocking Larger images will be block averaged or down sampled to fit within this size In the upper right corner of the image is a large blue square which shows a mag nified view of the pixels under the cursor position Go to the Pan Mag accelerator menu button Drag down and release on Display Panner The upper right corner now shows a reduced size version of your entire image The cyan box shows the area currently appearing in the display To change the area in the display click in side the cyan box with the left mouse button and drag the box to the desired area 54 CHAPTER 11 SAMPLE SESSION 55 of the image Release the left mouse button and the display will shift to show this section o
43. l however the more in teresting operations of learning and production as well as many of the tools will only work on VIEW format images The Format Conversion program under the Tools menu button can be used to convert a variety of image formats to VIEW format Save Image This button provides a simple interface for saving images Click and release the left mouse button to bring up a dialog box You can then directly type the image filename into the pink entry box or click on the red builder button to the left of the entry box to invoke a file browser Images can be saved in either VIEW or FITS format Click with the left mouse button to select the desired format Print Image This button provides an interface for printing images or saving as postscript Type the print command into the dialog box For example to send CHAPTER 2 JARTOOL BASICS 8 JAR ron mi t Californlo Institute of Technology JARtool 2 0 JPL Adaptive Recognition Teal i April 1997 ur PECE sonia ine 18 2666 Ja TA logia i i eg di la Ly Heda displayed sprepingn 54 wie clip ARL bagni Pigna a rpm lega fina Taa HA IITE maiae y ge Vele bi ITA Lone Magers 9 Figure 2 1 The JARtool graphical user interface the image to a printer called mammoth use lpr Pmammoth To save the image as a postscript file just type the filename e g tmp ps Destroy Image This button destroys the currently displayed imaged A popup
44. leading zeros will be used to maintain fixed width frame numbers For each frame number specified a filename is generated by concatenating the base filename the frame number and the filename suffix For example if the base filename is home venus image the frame numbers 1 3 and the suffix sdt then the List Expression tool would generate home venus imagel sdt CHAPTER 9 TOOLS 44 home venus image2 sdt home venus image3 sdt 9 3 Format Conversion The Format Conversion tool enables the user to convert several popular image for mats including VICAR FITS RAS RAS24 and PDS to the VIEW format re quired by JARtool Inputs input image list This parameter specifies the set of images to be converted The user can type the filenames separated by spaces into the entry box Path names are required unless the images are in the current working directory The user can alternatively specify a list file using notation Lists can con tain a combination of notation and explicit filenames The red builder but ton next to the entry can be used to construct or specify a list using one of several methods The format of each image in the input list is determined from the filename extension Currently supported input formats include VICAR vic FITS fits RAS ras RAS24 ras and PDS img Note that with SUN rasterfile RAS and RAS24 formats the converted images are greyscale even if the original images were indexed co
45. lor or RGB output image list This parameter specifies where to put the VIEW format out put images and how to name them The output image list can be a list of filenames the name of a directory or empty If empty the images are written in the current directory using their original base names but with the proper VIEW filename extensions Outputs The output consists of a set of VIEW format images which will be located on the file system according to the output image list parameter 9 4 JTRI Filter The JTRI Filter tool takes as input a list of jtri files and outputs a list of jtri files Each jtri entry is filtered according to criteria specified by the user For example a CHAPTER 9 TOOLS 45 typical request might be show me only those jtri entries which the scientists labeled as category 1 and which have radius larger than 20 pixels The filter for this example would have the following form L 1 amp R gt 20 0 The builder button for the filter entry generates two menus in a calculator format containing the allowed attributes that can be filtered and the allowed operations General algebraic expressions can be used as the basis of a filter operation For example SQRT H x W gt 20 0 where H is height and W is width T s JTRI Filter Parameters 380 r jtriattributes E i operators Lase R RADIUS DAR ac an bg W WIDTH H HEGHT 7 8 ti os pw it be X XPOS Y
46. model derived during learning to a new set of images with the goal of locating novel instances of the object of interest In this chapter we will provide a brief overview of the production algorithm and then focus on how to use the software For more details on the algorithm consult the references listed in the bibliography 8 1 Algorithm Overview The production algorithm consists of three components focus of attention FOA feature measurement and classification The FOA uses the matched filter derived during learning as a pre filter to screen local regions of each image Locations where the filter response exceeds a threshold are clustered together nearby hits are attributed to the same object The cluster centers are passed on to the feature measurement stage Feature measurement is performed on a region of interest ROI around each cluster center However the ROI is first normalized for variations in contrast level Feature values are measured by computing the inner product of the normalized ROI with the principal components templates obtained during learning Thus each ROI is converted from a high dimensional vector of pixel values to a low dimensional vector of feature values For each ROI the classifier assigns a class a posteriori probability based on the associated vector of feature values The probability values are thresholded and any ROl s with posterior probabilities exceeding the threshold are declared to be volcanoes
47. mylist in the Current selection entry box CHAPTER 11 SAMPLE SESSION 57 and click OK This will save your current list to file and bring you back to the XListE ditor Click OK here as well Notice that the image list parameter in the PIG is now set to the list you just saved The symbol tells the learning programs that mylist is not itself the name of an image but instead is the name of a file which contains image names We refer to this method of specifying a list as notation We also need to modify the jtri list Click on the red builder botton and select XListEditor Follow the same procedure as with image list i e under File load the default file Double click on ff20_consensus jtri to remove this entry from the Current List window Note that if you accidentally remove ff21_consensus jtri you can just double click on this entry in the third window to add it back to the cur rent list After you have properly deleted ff20_consensus jtri click on the OK button Since we didn t bother to save this list to a file all the list entries appear in the jtri list entry box Most of the entries scroll off the end but you can drag with the middle mouse button to see that they are really there The final thing to do before starting the learning process is to change the out put directory Click on the red builder button and select file browser Use the Hot Directories menu button to go to your home directory Type the name of a di
48. n Marker Popup Menu EENEN N e Note that the components designated as popup menus will not normally appear on the display These are activated by using the mouse buttons as described later Also there are six other components that you will encounter while using JARtool CHAPTER 2 JARTOOL BASICS 7 e Parameter Input GUI s PIG s e Entry Boxes e Builder Buttons e File Browser File Selection Box FSB e List Files e Busy Boxes e Marker Analysis Tasks 2 1 Accelerator Buttons The buttons along the left side of the JARtool interface are called accelerator but tons These buttons come in two varieties true buttons and menu buttons The menu buttons are distinguished by a series of dots following the button label To use the true accelerator buttons click with the left mouse button To use the accel erator menu buttons click and drag with the left mouse button Release the button when the desired option is highlighted Load Image This button provides a simple interface for loading images Click and release the left mouse button to bring up a dialog box You can then directly type the image filename into the pink entry box or click on the red builder button to the left of the entry box to invoke a file browser The preferred JARtool image format is VIEW format described in Appendix B Images in FITS Flexible Image Transport System format the native format of SAOtng can also be read and displayed in JARtoo
49. ne generates a file called class dbs in the database subdirectory under the production output directory This file is needed by the Insert Labels routine image list This parameter specifies the set of images in VIEW format to be used for testing The user may simply type the filenames separated by spaces into the entry box Pathnames are required unless the images are in the cur rent working directory The user may also specify a list file using notation Lists may contain a combination of notation and explicit filenames The red builder button next to the entry can be used to construct a list using a graphical interface or to look for a specific list that was previously stored in a file learning directory This parameter indicates the root directory where the model parameters generated during learning were stored i e the output directory specified during the learning process CHAPTER 8 PRODUCTION 41 user parameter file This entry should be the name of a file that sets up various user defined parameters that affect the production process e g the size of the ROT s the threshold applied to the FOA output etc The user can modify the parameters by copying the default file and changing it with a text editor such as emacs Changing this file is only recommended for experienced users Re fer to Appendix E for more information output directory This entry specifies the root directory that will contain the re s
50. nto JARtool CHAPTER 11 SAMPLE SESSION 62 Listing Labels If you list all the records in the LabelsWCS view it will list all the labels in WCS coords the LabelsPIX view lists all the labels in pixels First load ff05 sdt into the JARtool display area One way to do this is to list all the image files and click on ff05 sdt Click LabPx Img Auth An SQL query will be displayed which you must edit Substitute define IMAGENAME lt IMAGENAME gt define AUTHORNAME lt AUTHORNAME gt with define IMAGENAME jartool data images ff05 sdt define AUTHORNAME saleem Remember to replace jartool with the proper path to the JARtool root directory Click Execute and all the labels drawn by saleem on ff05 sdt will be listed Click Display Regions and the labels will appear on the JARtool display The color is dependent on the value of the LabelName field This value can be changed under the Regions menu button For example to compare the labels of two authors you might display one in red and the other in green Also all fields which do not describe the shape position or size of the marker will be attached as text The attached text can be hidden by selecting Toggle Marker Text from the Labeling menu in JARtool The listed regions can also be saved to a JTRI file From the Regions menu on the Query Tool select Save Results as JTRI file enter the desired output filename and click Ok Listing Objects From the
51. ol data labels ff20_consensus jtri Click on the OK button Zoom out so that you can see the whole image in the dis play The circles show all the volcanoes labeled by a pair of scientists The colors of the circles indicate the scientists confidence while the sizes correspond to their estimates of the volcano diameter To visually compare the scientists labeling with yours click on the Blink Frames accelerator button This will toggle the display back and forth between your labels CHAPTER 11 SAMPLE SESSION 56 and the scientists labels Click on the Blink Frames button again to stop the blink ing 11 5 Save Markers Go to frame 1 your labels using either the Prev Frame accelerator button or with the Goto frame 1 option under the Frames menu bar button Note that you may have stopped the blinking on frame 1 in which case you don t need to do anything The current frame number is displayed below the Frames menu bar button After reaching frame 1 save your markers by clicking on the Save Markers ac celerator button The default filename that comes up is inappropriate so you will need to select a new filename Click on the red builder button to bring up the file browser file selection box FSB Erase the text in current selection FSB by typ ing CTRL a CTRL k Now start typing the path to your home directory Unfortu nately the standard UNIX convention is not supported here As you type in the path the listboxes b
52. ontrol the magnification factor More details on the panner magnifier are given later in this chapter Colors This button provides a menu of colormap options Click and hold the left mouse button to see the options release on the desired option To change the display contrast and average brightness simply click the right mouse button on the image display area and drag until you get the desired re sult You must click outside of any defined markers otherwise the program will think you are selecting a marker Scaling This button provides a menu of scaling options Click and hold the left mouse button to see the options release on the desired option These trans form the pixel values before the colormap is applied Normally the default linear scaling should be used Coords This button provides a menu of coordinate display options Click and hold the left mouse button to see the options release on the desired option CHAPTER 2 JARTOOL BASICS 11 Normally the default pixels should be used There is also an option to turn off the display of the cursor coordinates Messages This button brings up a text window which shows various messages generated by the JARtool and SAOtng procedures If something doesn t work as expected look here for additional information and also in the window from which the JARtool program was invoked Control Panel This button is a convenient SAOtng feature that allows
53. options Set Region Color set the color in which labels will be displayed in JARtool Display Regions if labels are displayed in the Results Window and an image is loaded into JARtool this will overlay the labels on the displayed image Save Results as RGN file if labels are displayed in the Results Window this will save them to a RGN format file Save Results as JTRI file if labels are displayed in the Results Window this will save them to a JTRI format file Save Results as JTRI list if JTRI files are displayed in the Results Window this will produce a text file containing a list of the JTRI files This feature is useful since the learning routines and many of the tools operate on lists of JTRI files CHAPTER 6 DATABASE 34 6 3 Results Window This window is used by the Query Tool to display the results of user performed queries If the results are too large too wide or too many results scroll bars will appear which can be used to bring more information into the display area 6 4 Results Buttons This part of the interface contains some results related buttons The buttons and the functions they perform are as follows Clear Results clear the Results Window Save Results save the displayed results to a text file Display Regions if labels are displayed in the Results Window and an image is loaded into JARtool this button will display all the labels that lie on the dis played image D
54. opup menu contains options to control the behavior of the accelerator button There are three options 1 display the query in the Query win dow 2 execute the query and display results without displaying the query itself and 3 display both the query and the results To activate this menu move the cur sor over an accelerator button and hold down the right mouse button To select an option drag the mouse over the desired option and release The available options are Display Query display in the Query Window the query associated with the se lected accelerator button Display Results execute the query associated with the selected accelerator but ton and display the results in the Results Window Display Query and Results display in the Query Window the query associated with the selected accelerator button execute the query and display the results in the Results Window Set Default Action change the default action of the selected accelerator button to one of the above Remove Query remove the accelerator button Chapter 7 Learning The Learning menu button provides access to the JARtool learning capability which can be used to build appearance models for objects of interest given training exam ples In this chapter we will provide a brief overview of the learning algorithm and then focus on how to use the software For more details on the algorithm consult the references listed in the bibliography 7 1 Alg
55. or edit ing the file UNIX tilde notation The standard convention that a tilde represents a user s home directory and a tilde in front of a username represents that user s home direc tory is not supported in JARtool Menu Bar Submenus Disappear The menu bar submenus disappear if there is no image in the current display area e g if an image load fails or if the Destroy Image accelerator button is used Loading an image will cause the submenus to reappear Hypertext Help From the middle of one help page if you follow a hyperlink to another help page and then hit Prev to go back you are returned to the top of the first page rather than your previous point midway through the document FOA and Classifier Scores Not Included in JTRI Files The jtri file format does not easily permit the inclusion of extra information such as the scores produced by 74 APPENDIX F KNOWN BUGS IN JARTOOL 75 the focus of attention FOA or classification algorithms Hence the only way to see the results at different threshold settings is to modify the production_user pars file and rerun production If the scores were included in the jtri files then one would have been able to run the system at low threshold settings and use the JTRI Filter tool to interactively determine good thresholds Another consequence of this bug is that the VALUE attribute is not supported in JTRI filter or Chip Mosaic Query Tool Resizing and Scrolling Resizing the Que
56. orithm Overview The learning algorithm consists of three components focus of attention FOA fea ture learning and classification learning The FOA is intended as a quick pre filter to eliminate areas of an image that clearly do not have any volcanoes The output of the FOA is a discrete set of can didate locations which the algorithm has deemed to be worth examining in more detail The feature learning component uses principal components analysis to infer fea tures from statistical regularities in the training examples The types of features that can be learned are restricted to linear combinations of the pixel data Thus each feature can be viewed as a 2 dimensional template or mask The inner product correlation of the template with a region will be defined as the value of the fea ture The classification learning component is used to determine the mapping from vectors of feature values to class identity volcano or not volcano Classification learning is accomplished using a standard 2 class supervised technique The algo rithm uses labeled feature vectors from both the volcano and not volcano classes The not volcano examples consist of any objects that passed the FOA test but weren t 36 CHAPTER 7 LEARNING 37 designated by the geologists as possible volcanoes 7 2 Running the Learning Software From the Learning menu button select the LEARNING option This action will bring up a PIG parameter input GUI
57. owing files 1 saord tar gz the SAOtng source code 2 postgres tar gz the Postgres source code 3 jartool tar gz the JARtool source code and follow these steps 1 Install SAOtng on your system as follows a b f g Create a directory where you would like to install SAOtng From here on this directory will be refered to as SAOtngHome gt mkdir SAOtngHome Move the saord tar gz file to AOtngHome gt mv saord tar gz 5 AOtngHome Change directory to 5 AOtngHome gt pushd SAOtngHome Uncompress the saord tar gz file gt gunzip saord tar gz This command will produce a saord tar file Unpack the saord tar file gt tar xvf saord tar This will produce a saord subdirectory Change directory to saord Doc and follow the instructions in the BUILD file Note that you do not need to install the IRAF tools Also you should not do make strip keep the source code around After installing SAOtng you must put S AOtngHome saord bin in your path 67 APPENDIX A JARTOOL INSTALLATION 68 h Change directory back to the directory where you downloaded the tar files gt popd 2 Next you must install Postgres on your system To do this a b c d e f g h Create a directory where you would like to install Postgres From here on this will be refered to as PostgresHome gt mkdir PostgresHome Move the postgres tar gz file to PostgresHome gt
58. play the available jtri attrbiutes and operators in a calculator format Note If no expression is specified the value 1 will be associated with every chip To turn off the displayed text use the Toggle Marker Text option under the Labeling menu button arrange This option allows the user to rearrange the chip display based on the associated values Natural means use the order of the chips as they appear in the jtri list 1 e no sorting is applied CHAPTER 9 TOOLS 49 Outputs The output is a mosaic image that will be displayed in the current frame along with associated text values Use the Toggle Marker Text option under the Labeling menu button to turn off the displayed text if desired 9 8 Thumbnail Given a list of images this function creates an image of thumbnails in which each image is shown at reduced size The Thumbnail tool is useful for browsing a large number of images at low resolution Inputs image list This parameter specifies the set of images in VIEW format from which the thumbnails will be created The user may simply type the filenames sepa rated by spaces into the entry box Pathnames are required unless the images are in the current working directory The user may also specify a list file using notation Lists can contain a combination of notation and explicit file names The red builder button next to the entry box can be used to construct or specify a list using one of several available met
59. r Popup Menu There are also options in these menus to turn off the panner magnifier display and to set the magnification factor 2 4 Panner Magnifier Popup Menu In order to activate the panner magnifier popup menu position the cursor inside the panner magnifier and hold down the right mouse button To select an option drag the mouse so that the desired option is highlighted and then release the mouse button The available options enable a user to change the color of the panner magnifier toggle between panner and magnifier or completely hide the panner magnifier win dow 2 5 Image Display Area When JARtool is started the display is filled with an image of an area on Venus near latitude 30N longitude 330E The image also shows the JPL logo and the current JARtool release number New images can be loaded from either the Load Image accelerator button or from the Images menu bar button The size of the display can be increased by resizing the JARtool window 2 6 Coordinate Display Near the lower right corner of the image display area there may be a small window in which cursor coordinates are displayed This display can be turned off from the Coords accelerator menu button or theCoordinate Display Popup Menu 2 7 Coordinate Display Popup Menu In order to activate this popup menu position the cursor over the coordinate display Drag with the right mouse button until the desired option is highlighted and then release the mouse bu
60. rd See Chapter 5 for more in formation on markers New Frame This button provides a shortcut for creating a new image frame See the Frames menu bar button in Chapter 4 for more information Next Frame This button provides a shortcut for displaying the next image frame in the JARtool image area Invoking Next Frame from the highest numbered frame will go to the lowest numbered frame rather than create a new frame If you want to create a new frame use the New Frame accelerator button Prev Frame This button provides a shortcut for displaying the previous image frame in the JARtool image area Invoking Prev Frame from the lowest num bered frame will go to the highest numbered frame Blink Frames This button provides a shortcut for blinking between all the dis played image frames The control panel provides additional blink options in cluding controls for the blink rate and the frames to blink between Zoom In This button provides a shortcut for zooming in around the central point of the image display Zoom In multiplies the current zoom setting by a factor of 2 See also the Zoom accelerator menu button Zoom Out This button provides a shortcut for zooming out around the central point of the image display Zoom Out multiplies the current zoom factor by 1 2 See also the Zoom accelerator menu button CHAPTER 2 JARTOOL BASICS 10 Zoom Flip This button provides a menu of zooming options Click and
61. rectory to use for the output of learning say learning_test Click the OK button of the file browser Now you are ready to run learning Click on the OK button of the Learning Parameters PIG You should immediately see a busy box which contains a blue jar filling with water The busy box indicates that the learning process is running It may take a while 1 10 minutes to run learning depending upon the processing speed and memory of your machine If you are interested in your progress the win dow from which you started JARtool will show some checkpoint messages from the learning procedure When learning is finished the jar of dripping water will disap pear 11 7 Production Click on the Production menu bar button and select the PRODUCTION option This action will bring up the Production Parameters PIG You will need to change some of the parameters To do this you can use the builder buttons or type directly into the entry boxes e Change the image list entry to jartool data images ff20 sdt where as usual jartool should be replaced by the path to the toplevel directory CHAPTER 11 SAMPLE SESSION 58 where JARtool is installed Note that there should not be an sign in front because this is itself the name of an image e Change learning directory to your_home learning_test where your_home is the path to your home directory e Change the output directory to your_home production_test e Make sure that the A
62. rs Asker Kevin Cherkauer Victoria Gor Steve Hyland John Loch Mike Turmon and Jennifer Yu Research and development of the system described in this manual was carried out in part by the Jet Propulsion Laboratory California Institute of Technology un der contract with the National Aeronautics and Space Administration 64 Bibliography 1 M C Burl L Asker P Smyth U M Fayyad P Perona J Aubele and L Crumpler Learning to Recognize Volcanoes on Venus in review September 1997 2 M C Burl U M Fayyad P Perona and P Smyth Trainable Cataloging for Digital Image Libraries with Applications to Volcano Detection CNS Tech Report CNS TR 96 01 Calif Inst of Technology October 1996 3 U M Fayyad P Smyth M C Burl and P Perona Chapter Learning to Cat alog Science Images In Early Visual Learning Oxford University Press pp 237 268 1996 4 M C Burl U M Fayyad P Perona P Smyth and M P Burl Automating the Hunt for Volcanoes on Venus In EEE Comp Society Conf on Computer Vision and Pattern Recognition pp 302 309 Seattle WA June 1994 65 Part III Technical Appendices 66 Appendix A JARtool Installation In order to install JARtool first make sure that you have the appropriate Tcl Tk code wish4 2 and tclsh7 6 or newer installed on your system Also be sure that the directory containing the wish executable is in your path Next download the foll
63. ry Tool to incease the amount of text displayed in the Results Window does not work properly due to a bug in the Tk text widget There may also be slight errors in the text scrolling e g only half the bottom line may be visible due to the same bug Database Deletions Users must be extremely careful when deleting records rows from any of the database tables because these operations may affect other tables Postgres does not support triggers so the effects upon other tables cannot be prop agated appropriately Consider for example deleting a row from the Hometown ta ble discussed in Chapter 6 The Hometown ID_number for the deleted row may still appear in other tables such as the Employees table These other tables will now contain stale and or corrupted data
64. s tasks Click the right mouse button inside or on the boundary of a marker and drag down to the Marker Analysis Tasks menu option This action will bring up a submenu with a variety of functions The avail able options are dependent upon the marker type For example with line markers it is possible to plot the intensity profile along the line With box markers you can find statistics of the pixels inside the box Users can also add their own marker anal ysis routines by following the examples in the manalysis cmds file under the CHAPTER 2 JARTOOL BASICS JARtool directory structure jartool saotng cmds 22 Chapter 3 Images The Jmages menu button provides options for loading saving and printing images To load an image click the left mouse button and pulldown the options menu Re lease the button over the Load Image option and type the image filename into the entry box Instead of typing into the entry box you can click the left mouse but ton on the builder button to the left of the entry box This will invoke a graphical file browser that can be used to select the filename After hitting OK the selected filename will be loaded into the image area The preferred JARtool image format is VIEW format however the native im age format of SAOtng is FITS Flexible Image Transport System a format which was developed within the astronomy community FITS format images can be read and displayed in JARtool however the learning
65. sion of the basic SAOtng marker format Appendix C contains more details on the JTRI file format Chapter 6 Database The Database menu button is used to invoke the Query Tool a graphical user in terface for interacting with the JARtool database Before using functions in this chapter the database must be up and running Appendix A contains the database installation instructions With the Query Tool the user can e Insert and update information in the database e Retrieve information from the database using SQL queries e Save the retrieved information e Visualize retrieved information Information in the database is organized into structures called tables Each table has a number of attributes One can think of the attributes as column headings For example in an employee records database we might want to store an employee ID number employee name and date of hire These would be the attributes and each employee would be represented by one row in the table Now suppose we wanted to also keep track of the employees hometown There are several ways this could be done We could simply add to the table a column containing each employee s hometown as a text string e g Pasadena However this is somewhat inefficient for storage and indexing since the same hometowns would be repeated frequently An alternative is to make a second table containing a hometown ID number and a hometown string To the first table we would add a
66. t boxes are three buttons used to return from the FSB quit or get help documentation Ok Cancel and Help Hot Directories Clicking and holding the left mouse button on Hot Directories will bring up a pull down menu of hot directories Releasing the mouse button over one of these items will place it in the current selection and update the listboxes accordingly Releas ing the mouse button over the Add Entry menu option will add the directory from the current selection entry box to the list of hot directories If the current selection refers to a file rather than a directory the directory path to the file will be stripped off and added to the list CHAPTER 2 JARTOOL BASICS 17 y JARtool File Browser 7 Current selection proj mgn sar2 jartool data images ff20 sdt Current template jartool data images ia AL Ap A emacs_saleem Fimages ff05 fits Makefile labels ff05 sdt analysis learning ff05 spr productions ff13 sdt jartool ff13 spr saotng 1a scripts ff20 spr ff21 sdt ff21 spr ilist f Ei AY r W r WN p Ok Cancel Help Figure 2 3 JARtool file browser file selection box E L Programmers Note The file containing the set of hot directories can be spec ified through a command line flag dirs when the FSB is invoked If this flag is omitted the FSB checks the current working directory for a file named user directories If that file doesn
67. te and return the current selection to the calling program Hitting the Return key while in the current selection entry box performs the same function Cancel Clicking the mouse on the Cancel button will cause the FSB to terminate and return a null selection to the calling program CHAPTER 2 JARTOOL BASICS 20 Help Clicking the mouse on the He p button will cause a hypertext help file to be dis played 2 17 ListFiles List files are simply ascii files with one item per line For example the following items the names of four image files could stored in a list file called old4 home venus ff05 sdt home venus ff13 sdt home venus ff20 sdt home venus ff21 sdt List files can be used whenever a parameter expects a list of items The sym bol must be placed infront of the list filename so that JARtool knows to get the file names from within the list file This convention is called notation Thus if an entry box asks for a list of images the following specifications are equivalent 1 home venus ff05 sdt home venus ff13 sdt home venus ff20 sdt home venus ff21 sdt 2 old4 The list file method of specification can be mixed with explicit filenames as in the following example e Qold4 home venus ff32 sdt Note that this specification contains five images the four listed in old4 plus ff32 sdt 2 18 Busy Boxes Several functions in JARtool such as learning can take some time to complete To let the
68. ted by spaces The appropriate tables will be updated in the database Insert Images insert images into the database You will be asked to provide the name of a file The file will contain a number of lines and each line will have an image filename minimum latitude maximum latitude minimum longi tude maximum longitude image height image width and look direction all entries separated by spaces The appropriate tables will be updated in the database CHAPTER 6 DATABASE 32 Clean Database remove all records from the entire database proceed with cau tion Disconnect disconnect from a database server Quit exit from the Query Tool Tables This menu contains the following options List Tables list all the tables in the active database List Attributes list the attributes column headings of a particular table List Records list the records rows of a particular table Clean Objects Table delete all object related information from the database Update Objects Table re create the objects table and update all other tables which have object related attributes Views Menu This menu contains the following options List Views list all the views in the active database List Attributes list the attributes column headings of a particular view List Records list the records rows of a particular view Query Menu This menu contains the following options Clear Query clear t
69. the user to control many elements of the display from a single interface It also includes more options to control blinking between frames Quit This button exits from JARtool 2 2 Menu Bar The menu bar consists of the buttons near the top of the display Clicking and hold ing the left mouse button on a menu bar item causes a pulldown menu to be dis played To select an option from the pulldown menu drag the mouse to the desired option and release To avoid selecting any options release the mouse button while the cursor is not on the menu The menu bar contains the following functions These buttons will be discussed in greater detail in Chapters 3 10 respectively e Images e Frames e Labeling e Database e Learning e Production e Tools e User Cmds 2 3 Panner Magnifier Near the upper right corner of the image area there may be a small window with a special cursor This window can serve as either a panner or magnifier As a panner the window shows a reduced size version of the entire image The user can manip ulate the view by clicking and dragging the cyan box in the panner window with the CHAPTER 2 JARTOOL BASICS 12 left mouse button An alternative method of panning is to click the middle mouse button on the image display As a magnifier the window shows a closeup of the image area under the cursor To switch between panner and magnifier use the Pan Mag accelerator menu but ton or the Panner Magnifie
70. tngHome HOSTNAME HOST Install all the executables gt make install PSQL PostgresHome SAOTNG SAOtngHome HOSTNAME HOST Clean up gt make clean Put the J ARtoolHome directory in your path Change directory back to the directory where you downloaded the tar files gt popd Appendix B VIEW Format Images used by the JARtool learning and production components are required to be stored on local disk in what is known as VIEW format This format consists of two files per image The ASCII spr file contains header type information number of dimensions number of rows number of columns data type etc while the binary sdt file contains the pixel data When supplying image names to any of the various JARtool routines specify the filename with the sdt extension Here is a sample spr file 2 1024 0 000000 1 000000 1024 0 000000 1 000000 0 0 000000 0 000000 This file indicates that the data is 2 dimensional 1024 X 1024 and in byte format 0 The real valued numbers originally were used to designate the origin and sam ple spacing but these are no longer supported 69 Appendix C JTRI Format Labeling information provided by scientists or generated by automatic algorithms is represented in JARtool using jtri format This format evolved from the native region format used in earlier versions of SAOimage The jtri format contains one row for each detected or labeled object A typical entry might be as follows C
71. to just typing the values into the entry box Clicking the left mouse button on the builder button will bring up a menu of builder options For example if a list of images is needed as a parameter clicking on the builder button will bring up a menu with options to 1 build a list with the XListEditor graphical interface or 2 build a list with the List Expression tool or 3 invoke a file browser to look for a list that was previously stored on the file system 2 16 File Browser File Selection Box FSB The File Browser File Selection Box FSB provides a convenient interface for the user to browse through the file system and identify filenames or directories for use as PIG or dialog box inputs The user s selection appears in the entry box area labeled Current Selection Clicking the mouse on the Ok button near the bottom of the interface or hitting a carriage return while in the entry area will send the current selection back to the calling program and terminate the FSB Physical Layout The FSB consists of several components arranged in the following way Near the top of the interface are two dark blue buttons labeled Hot Directories and Tem plates Below these buttons are two entry box areas labeled Current selection and Current template The main body of the interface is a set of three list boxes The list boxes show the hierarchical directory structure associated with the current selection Below the lis
72. tton CHAPTER 2 JARTOOL BASICS 13 The available options enable the user to specify the units the coordinate sys tem to be used if multiple coordinate systems are specified in the header of a FITS image and the color of the coordinate display 2 8 Colorbar Slightly below the image display area there is an elongated bar that shows the map ping between pixel values and color The image colormap can be modified by click ing and dragging the right mouse button within the image display area outside of any marker symbols To restore a standard colormap use the Colors accelerator menu button or the Colorbar Popup Menu 2 9 Colorbar Popup Menu In order to activate this popup menu position the cursor above one of the numbers drawn on the colorbar Hold down the right mouse button To select a menu option drag the mouse until the desired option in highlighted and then release the mouse button The available options enable the user to specify the color of these numbers 2 10 Text Information Beneath the colorbar is a small area used for text display Typically this area con tains the name of the displayed image and other information about the section of the image currently being displayed 2 11 Help Button At the lower left of the display is a help button that provides access to hypertext documentation The documentation is divided into JARtool and SAOtng Click with the left mouse button on any highlighted words to get more in
73. ults of production i e the jtri files containing the detected object locations This directory and its subdirectory structure will be created if it does not al ready exist If the directory and subdirectory structure already exist the con tents may be overwritten Outputs The output of production is a set of jtri files containing the coordinates of each de tected object If the Auto Display flag is on the results will be displayed in con secutive frames If the Auto Insert flag is on the results will be inserted into the appropriate tables of the database Chapter 9 Tools 9 1 XListEditor Many components of JARtool are structured to work on lists of images or lists of Jtri files The XListEditor enables a user to construct lists using an interface similar to the File Browser File Selection Box Lists can be saved in files and then supplied to programs using notation This approach is often more convenient than typing all the image or jtri names into an entry box The XListEditor contains three listboxes that allow the user to browse around through the directory structure In addition there is a fourth list box that is sepa rated slightly from the others This box maintains a list of the items that have been selected by the user To add an item to the current list double click on the item in one of the first three listboxes To remove an item double click on it in the fourth listbox On the XlistEditor under the File pulldo
74. user know that these processes are runnning and to provide a mechanism for aborting a running process the JARtool system starts up a busy box for selected time consuming functions The busy box will appear as a jar that is continuously filling with water Unfortunately the fill rate is not proportional to the progress of the function so a jar may fill and empty many times before a function is completed The user can abort a function by clicking on the Quit button of the appropriate busy box This action will kill the function and any background subprocesses it may have spawned CHAPTER 2 JARTOOL BASICS 21 oa Eusy Box LEARNING pa Jartoal Quit is pa Figure 2 4 Busy box for learning Warning There is a potential bug with the busy box kill button When clicked the busy box does a ps l system command to list currently running processes and then it tracks down all children of the primary process However in the time between performing the ps command and the time when the child processes are killed it is possible that new processes could have been spawned These new pro cesses will not be killed Programmers Note Another potential hazard is the fact that the child_processes procedure is based in part on the format of the UNIX ps l output as it appears on SUN workstations This dependency could lead to problems if JARtool is ported to other platforms 2 19 Marker Analysis Tasks SAOtng now supports marker analysi
75. uto Display control flag is turned on If the square but ton next to Auto Display is raised click to turn the flag on e Also make sure that the Auto Insert control flag is turned on After all the parameters are set properly click on the OK button of the Pro duction Parameters PIG You should immediately see a jar filling with water to indicate that production is running When production is completed the ff20 image will automatically be displayed in the next available frame frame 3 if you have been following along through the example Use the Zoom out accelerator button to see the entire image There should be be a set of red and blue squares overlaid on the image All squares correspond to areas that the focus of attention FOA algorithm identified as interesting The blue squares however were rejected by the classifer as non volcanoes while the red squares were declared to be volcanoes There is a threshold in the production user parameter file that can be adjusted to make the classifier more aggressive or more conservative 11 8 JTRI Filter To see only the red squares go to the Tools menu and select the JTRI Filter op tion The default entry for jtri list is sao which tells the system to get the cur rently displayed markers The default output is also sao which tells the system to put the filtered markers back on the display The default filter expression is L 1 which selects only those markers that ha
76. ve a label equal to 1 Since the red squares have label 1 we can just use the default settings Click on the OK button The marker overlay will be redrawn with only the red squares Save the JARtool markers to a file using the Save Markers accelerator button Save the JARtool markers as your_home JAR_markers jtri 11 9 Chip Mosaic Under the Tools menu select Chip Mosaic This action will bring up a Mosaic Parameters PIG Click on the red builder button next to expression to bring up a CHAPTER 11 SAMPLE SESSION 59 calculator style menu of jtri attributes and operators You may need to move the at tributes and operators menus around slightly on your workspace to see both Click on LABEL in the attributes menu The letter L will appear in the expression entry box Go back to the PIG and click the ascending option one of the buttons next to the arrange parameter Next click the OK button of the PIG The tool will generate a collage of chips which were extracted from locations identified by the scientists as potential volcanoes The subjective confidence labels assigned by the scientists are shown in cyan Notice that we have displayed the chips in ascending order by label If the contrast of the displayed image is not so good you can modify it by moving the cursor into the display area and dragging with the right mouse button until the contrast is satisfactory You can toggle the display of the text by selectin
77. ver the entire im age See also Marker Analysis Tasks in Chapter 2 10 2 Image Mean and Standard Deviation This function computes the mean and standard deviation of the data values over the entire image See also Marker Analysis Tasks in Chapter 2 10 3 Image Histogram This function computes a histogram of the data values from the entire image The resulting graph is displayed with a utility called xgraph 10 4 Adding New Commands Users can easily add their own commands to the User Cmds menu The procedure works as follows 1 Edit the analysis cmds file which is located in jartool saotng cmds 51 CHAPTER 10 USER COMMANDS 52 2 Copy and paste the code for one of commands listed above e g Image His togram 3 Change the first line of code from Image Histogram to the name for your new routine as you want it to appear in the menu 4 Change the fourth line to contain the name with path of your callback The callback is the executable program or script that will be invoked when the user selects your menu option 5 Your program or script can operate on the image and or markers displayed in the current frame and can send results back to the display Refer to the hypertext SAOtng documentation for complete details Part II Sample Session 53 Chapter 11 Sample Session We describe here a sample session with the JARtool system You may want to try out these examples to get a feel for what you can do w
78. wn menu button there are options for saving the current list to file loading a list from file and clearing the current list 9 2 List Expression The List Expression tool allows the user to specify a list of files having names like imagel sdt image2 sdt image3 sdt etc The user provides a base file name a set of frame numbers and a filename suffix The frame numbers may be a comma or space separated list Note the use of the word frame in this con text is unrelated to the Frames discussed in Chapter 4 Colon notation i e start_frame increment end_frame is also supported For example 0 5 20 would spec ify frames 0 5 10 15 and 20 The increment may be omitted in which case the de 42 CHAPTER 9 TOOLS 43 r JARtool List Editor g Current selection proj mgn sar2 jartool data images ff21 sdt Current template Sct jartool data images Current List Nit AL 8 A jartool data images ff05 sdt analysis ages ff05 sdt jartool data images ff13 sdt labels PP13 sdt jartool data images ff20 sdt saotng learning PP20 sdt scripts production ff21 sdt Ok Cancel Help a Figure 9 1 The XListEditor provides a graphical interface for constructing lists which are used by many of the JARtool functions fault value is 1 Negative increments are permitted If the start_frame is given as 001 or some similar fixed width expression with leading zeros and the end_frame is of the same width then
79. ws list the views in the active database Attr Table list the attributes column headings of the specified table List Table list the records rows of the specified table Img Obj list the images which contain the specified object Img Lat Lon list the images which contain the specified point on the planet ImgRgn Auth list the images and the region files produced by a specified author or set of authors RgnAuth Img list the authors who labeled the specified image and the names of the region files produced Obj Img list all objects from the specified image Obj Lat Lon list all objects in a specified area of the planet CHAPTER 6 DATABASE 30 _ i le e _ JE Query Tool ees Databases Tables Views Query Results Images 2 mgnsar2 LabelName Tables Figure 6 1 The Query Tool graphical user interface Obj Auth list all the objects labeled by the specified author LabPx Img Auth list all labels in pixel coordinates that were produced for the specified image by the specified author LabWCS Img Auth list all the labels in wcs world coordinate system coor dinates that were produced for the specified image by the specified author LabPx Rgn list all the labels in pixel coordinates from the specified region file LabWCS Rgn list all the labels in wcs coordinates from the specified region file CHAPTER 6 DATABASE 31 Auth Obj list all authors who la
80. ystem 11 11 Database Getting Started To start the query tool select Query Tool from the Database menu on JARtool The database must already be up and running Refer to Appendix A for instructions on setting up the database Next connect to the Sample database by choosing the ap propriate option from the Databases menu on the Query Tool Listing Images From the Views menu on the Query Tool activate the List Records submenu From this submenu select ImageFiles This should list all the records in the images table there are only four Each record should contain the name of the image the latitude and longitude range and the look direction If you would like to view all of the listed images select Display Images from the Images menu on the Query Tool This will load the four images into four dif ferent frames One can also save the results as an image list file Select the Save Results as Image List option from the Jmages menu on the Query Tool Enter the save file name and click the Ok button CHAPTER 11 SAMPLE SESSION 61 Besides listing all the images one can also list images which satisfy a particular criterion Click on the Img Lat Lon accelerator button This will display an SQL query in the Query Window Edit the text in the Query Window You will need to substitute actual values for the lt LAT gt and lt LON gt placeholders Original define LAT lt LAT gt define LON lt LON gt After

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