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Workshop at the19 th Biennial Conference on the Biology of Marine Mammals

Workshop at the19 th Biennial Conference on the Biology of Marine Mammals. Learning to effectively and efficiently use DARWIN ( D igital A nalysis and R ecognition of W hale I mages on a N etwork ) John Stewman and Kelly Debure Eckerd College, St. Petersburg, FL

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Workshop at the19 th Biennial Conference on the Biology of Marine Mammals

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  1. Workshop at the19th Biennial Conference on the Biology of Marine Mammals Learning to effectively and efficiently use DARWIN ( Digital Analysis and Recognition of Whale Images on a Network ) John Stewman and Kelly Debure Eckerd College, St. Petersburg, FL http://darwin.eckerd.edu/19thBiennialWorkshop.ppt

  2. Lots of examples Workshop Overview • Software overview • Software installation • Creating a custom catalog scheme • Building a catalog (database) • Comparing sighting images to the • catalog • Creating a list of images to match against • the catalog • Backup and restore of database • Exporting data for use with other software Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  3. Software overview • DARWIN is a software system that: • provides access to a collection of digital FINs • (each containing digital images, dorsal fin • outlines and various textual data) • allows users to query the FIN database for the • identity of a dolphin in a new dorsal fin image • allows users to query the system with the name • of a specific individual • allows users to sort and view a collection of FIN • images based on sighting location, sighting date, • location or damage category Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  4. Software installation (Windows) • Insert the CD • Double-click darwin-2.22-setup.exe • A dialog should appear as at left. Check the box to accept the license agreement • Click “Next” • 5. The default installation directory is shown • To change the installation directory, click Browse, select the desired directory, click OK, and the new path will appear with “darwin-2.0” appended. It is best to leave “darwin-2.0” appended to the path. • NOTE:Windows Vista and Windows 7 users should NOT install in the Program Files folder. • 8. Click “Install” Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  5. Software installation (Mac) • Insert the CD • Double-click the disk image file --darwinMac2.22Installer.dmg • The installer should open showing the darwinMac.app application and a readme file • Drag the dawinMac.app application to your Applications folder, your desktop or wherever you desire it to reside. • Drag the readmeMac.txt file to your desktop as well. • Close the Installation folder, eject the disk image, and eject the CD. • 8. You are ready to go. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  6. Running DARWIN Initially, when the software runs, the database area of the main window will come up empty since no database is available to display. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  7. Creating Your Own Catalog Scheme To create your own catalog scheme, select “Define New Scheme” from the “Settings > Catalog Scheme” menu Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  8. Creating a Catalog Scheme • A dialog should appear, as shown. • Click in the top text entry area to enter a name for your custom Catalog Scheme • Click in the text entry area below that to enter a name for each category for your catalog scheme. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  9. Using a Custom Catalog Scheme The Active catalog scheme is the default scheme for creating any new catalog. A catalog created with one scheme cannot be converted to another scheme. To activate your own catalog scheme, select “Select Active” from the “Settings > Catalog Scheme” menu Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  10. Using a CustomCatalog Scheme • A dialog should appear, as shown. • Select your custom Catalog Scheme name from the list at the left • You should see your custom category names appear in the list at the right. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  11. Creating a Database • Select “New Database” from the “File” Menu • Select “New Survey Area and New Database” • (Generally you will want to create a new Survey Area for each new database you create.) • 3. Select the Catalog Scheme • (The catalog provides different damage categories with which searching can be restricted. The Eckerd College Scheme is always available but you can create your own catalog scheme through the “Settings” menu.) • Enter a Survey Area Name • Enter a database name (.db will be appended automatically) • 6. Hit “OK” Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  12. Creating a Database If you are creating a new Survey Area, you will have to select (or create) a data path folder to hold it. DARWIN now allows you to place the data anywhere. However, the data path folder must be named “darwinPhotoIdData” • If the data path folder already exists, simply select it and hit “OK” • If the data path folder does not exist, or you desire to have the new Survey Area somewhere else, then navigate to that location and Create a new folder named “darwinPhotoIdData” • Select it and hit “Save” Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  13. Adding a fin to the database • Select “Open Image” from the “File” menu • or simply click on the leftmost “open” button on the toolbar and a dialog will appear as shown at left. • Navigate to the folder where you have the images with which you would like to build a database. All available drives are listed in the area at the left. The path of the current folder is shown above the main area. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  14. Adding a fin to the database • The path of the current folder is shown above the main area. Select a file by clicking on it. • The name of the file will be highlighted and the image will be shown at right. • Click “Open” Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  15. Tracing a fin outline • The trace window appears when an image is opened. Tracing is a three step process. To access each step, simply click the buttons at the top of the window. • Once a new fin is opened, the program starts in the “Modify image” mode with the trace window enabled for a number of image enhancement options. • Tools above the image allow the image to be: • Zoomed (click to zoom in shift-click to zoom out) • Flipped (fins should swim to left) • Contrast enhanced • Brightened • Cropped • If no modifications to the image are desired, the user may simply click on the "Trace Outline" button. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  16. Tracing a fin outline • Once the “Trace outline” button has been clicked, the program enters tracing mode with the window tools enabled for tracing a fin outline. • Click a point on the leading edge of the fin, then click a second point on the trailing edge of the fin. The software will attempt to automatically extract the outline. • Tools above the image allow the outline to be : • Zoomed (click to zoom in shift-click to zoom out) • Re-traced by hand • Modified by the addition of points • Modified by the movement of points • Modified by the erasure of points • Chopped at either end of the trace • After completing any modifications to the outline, the user simply clicks the “Locate Features" button to proceed. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  17. Tracing a fin outline 1. Once the outline has been traced, the user may click on the “Locate Features" button. (This step is optional but can be useful to verify the positioning of the “tip” and view the complete outline.) 2. Enter information about the image in the text entry fields at the right. 3. Select a Damage Category from the dropdown list. 4. To add the fin to the database, click the “Add to Database” button. You do not need to click the “Save” button* to add a fin image to the database. (*Save is used to save the trace for queue processing and will be discussed later.) Improperly placed feature points may be manually repositioned. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  18. Tracing Difficulties: glare spots • Trace the fin as previously described. • Click on the “magnify” tool, then click in the area of the glare spot. • Use the “eraser” tool to remove the points which have been improperly located due to glare Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  19. Tracing Difficulties: glare spots • Use the “move” tool to move a point to the center of the glare. Points do not have to be filled in all along the edge since the software will do that automatically • Click on the “magnify” tool. Hold down the shift button while clicking on the image to zoom out. • Click “Locate Features” button to view resulting outline Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  20. Tracing Difficulties: hi-contrast waves • Trace the fin as previously described. • Click on the “magnify” tool and click on the misplaced outline points to zoom in. • Use the “eraser” tool to remove the points which have been improperly located along the wave. • Use the “move” tool to move a point from the outline to the center of the unlined area. • Click on the “Locate Features” button to view the repaired outline. • Click on the magnify tool. Hold the shift button down and click on the image to zoom out and view the complete outline. Sometimes the improperly placed points may simply be erased. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  21. Tracing Difficulties: hi-contrast waves • Click on the “contrast enhance” tool. • Use the slider bars to adjust the contrast. Moving the top slider to the left makes the dark areas darker. Moving the bottom slider to the left make the light areas lighter. • Click OK. • Trace the outline as before. • Certain areas along the outline still need to be repositioned. Sometimes contrast enhancement can help reduce the interference. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  22. Zoom in for as close a view as possible • Some images do not autotrace well at reduced scales. (50% versus 100%) • Zoom in to the closest view possible, for best autotrace. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  23. Verify outline and feature points Click on the “Locate Features” button to view your final outline and outline features before saving. This step is particularly important in images with splatter artifacts and whenever the outline has been hand manipulated by inserting or moving points in the outline. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  24. Autotrace if possible; sometimes it’s not • If too much of the outline needs correction just trace by hand using the “pencil” tool. • Don’t erase the misplaced outline with the eraser. Just click the “pencil” tool and then click the image. DARWIN will ask if you want to erase the previous trace. Click yes. • Then trace the new outline manually, holding the left button down as you trace. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  25. Importing a Catalog From the Main Window FILE/Import menu select Import Catalog Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  26. Importing a Catalog An Open File dialog will automatically take you to the DARWIN backups folder and list all available zipped archive files. You may change the folder as desired. Select the zipped archive file containing the catalog you want to import, and click Open. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  27. Importing a Catalog Import differs from restore. It requires you to place the imported catalog in a new survey area. This prevents the imported catalog from overwriting files in an existing survey area. The import will create ... - the new survey area and all its folders - the catalog database and all image files You will be prompted if conversion from a previous DARWIN catalog format is necessary. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  28. Opening a different catalog To open an existing catalog from a folder of your choosing, select “Open Database” from the File menu. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  29. Opening a different catalog The current path is shown at the top of the dialog. Navigate to the correct folder. Select the database (*.db) file to open. Click the “Open” button. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  30. Examining Images, Outline, and Data The Main Window lists all fins in the open catalog in the left pane. This list can be searched by ID, scrolled and sorted based on any column of data. The Main Window has tabs at the top of the right pane that allow the user to access information on the currently selected fin, The Original Image, Modified Image, Fin Outline, and Fin Data may all be viewed by clicking the appropriate tab. Larger versions of each image and fin outline can be opened by simply clicking the displayed image or outline Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  31. Modifying or Deleting a Fin In the Main Window, the selected fin in the current catalog may be deleted or modified. Just click the Modify button and then … Make any desired changes to sighting data and then do one of the following. Click Save (to commit the changes) Click Delete Fin (to remove the fin from the catalog) Click Cancel (to close the window without making any changes) Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  32. Tracing Difficulties: missed notches • Sometimes the autotrace operation misses significant notches and these may be captured by manual manipulation of the outline • Click on the “Move” tool (the hand) or the “Insert” tool (the red arrow) to capture the notch. • Zoom out after any manual adjustments (Shift-click with “Magnify” tool) • Click the “Locate Features” button to view the new trace. Insertion of points into the outline can be tricky. Insert the new point halfway between the two points between which you want the new point to fall, then drag it to its proper location. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  33. Matching a fin against the catalog After tracing the fin, click on the “Match” button in the trace window. The Matching Dialog will appear as shown here. Click “Select All” to match against the entire catalog or select categories individually to reduce search time. Click “Start” to start the matching process. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  34. The Match Results Window The Match Results Window shows a selected catalog fin and the unknown fin side by side It lists all matched catalog fins in order of best match to worst match, but the list can be sorted based on any column of data by clicking the column heading The user can select any catalog fin for side by side comparison by scrolling the list and clicking a fin, using the next and previous buttons, or by enabling the automatic scrolling Modified and original images and fin traces may be magnified for closer examination Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  35. The Match Results Window The user may add the new (unknown) fin to the database by clicking either button below Matches Selected Fin No Match – New Fin In the current DARWIN version there is no difference in their actions The user may Return to the Matching Window if this was an interactive match Match Results may be saved for viewing again later. The user may close the window by clicking Done Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  36. Tracing Difficulties: thick leading edge • Sometimes the camera angle causes the full thickness of the leading edge to be visible complicating the placement of the outline. • Either edge can be used for the outline without significant effect upon matching outcomes. • Often it is simplest just to retrace the entire fin manually. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  37. Tracing Difficulties: occlusions • If too much of a fin is occluded it can negatively impact the alignment process for comparison. • Often it works well to add a few points to indicate the likely position of the occluded edge Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  38. Saving Fins forQueued Matching Interactive matching from the Trace Window is fine in many instances, but when large numbers of sighting images are processed or the catalog contains many images, it may be desirable to create a queue for matching. • With queued matching: • multiple fins may be traced and • saved for later matching • multiple matches against the catalog • may be run unattended with results • automatically saved for later review • To trace and save a fin for later use, open the fin image, trace the outline and enter sighting info as before • Then, from the Trace Window click the Save button • Minimum requirements before save … • Fin trace must be completed • Dolphin ID field must be filled in Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  39. Saving a Traced Fin In the Save File dialog, accept or provide a name for the saved fin (the file extension “.finz” will be appended to the user supplied name) All saved fin traces (FINZ files) are saved in the tracedFins folder by default Finally, click Save Each saved FINZ file includes ... the actual fin trace all sighting data a copy of original image the DARWIN modified image Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  40. Matching Difficulties: long leading edge When a leading edge is elongated by the view or dolphin’s movement, it may be advantageous to tend toward a shorter trace. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  41. Matching Difficulties: missing tip • The position of the fin “tip” plays a significant role in the alignment of fins for matching. • One recommendation is to always be sure the “tip” point is located along the leading edge. If the software places it at the trailing edge, click on the “move” tool and drag the point to its desired location. • The point will turn red while moving. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  42. The Matching Queue From the Main Window FILE menu select Matching Queue The Matching Queue provides access to all queued matching capabilities and to all match results saved for later review Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  43. The Matching Queue A list of the names of previously saved fin files may be created using ... Add and Remove Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  44. The Matching Queue Matching queue actions include ... Run Match (performs matches of listed fins to the current catalog and saves results) View Results (loads previously saved results of a match of a fin to the catalog) Save Queue (saves the list of fin file names) Load Queue (loads a previously saved list of fin file names) Cancel (closes the matching queue window) Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  45. Viewing Saved Match Results From the Matching Window click the Start button to run an interactive match – the Match Results Window will appear automatically. Or open the Matching Queue Window by clicking the View Results button, select a results file, and click Open to view any previously saved match results. The Match Results window will list all matches in a ranked listing. Saved match results file names indicate the fin and the catalog to which it was matched ... TampaBay-DB-match-for-PAPI.res is a match of the fin trace for PAPI to the TampaBay catalog Saved match results files are in the MatchQResults folder within the same survey area as the fin file and the catalog Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  46. Saving Match Results Match results are always saved in the MatchQResults folder within the same survey area as the fin file and the catalog. The results files are named to indicate the fin and the catalog matched. For example … TampaBay-DB-match-for-PAPI.res is a match of PAPI to the TampaBay catalog From the Matching Queue Window clicking the Run Match button will run all matches listed in the queue and automatically save the results of each match However, from the Match Results Window after an interactive match, the user can click the Save Match Results button to save the results. If the fin was not already saved, this will cause it to be saved as well. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  47. Backup of a Catalog From the Main Window FILE menu select Backup All of the currently open catalog will be archived into a backup with a name indicating the survey area, the catalog, the date and a sequence tag if multiple backups are initiated on the same day Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  48. Backup of a Catalog Backup location: the backups folder Sample names: default_ECDP_Oct_01_2009.zip default_ECDP_Oct_01_2009[2].zip (Backups of the ECDP catalog in the default survey area on Oct 1, 2009) A backup contains all catalog images the catalog database file (*.db) A backup does NOT contain saved fin traces in the same survey area saved match results related to the catalog Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  49. Restoring a Catalog From the Main Window FILE menu select Restore Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

  50. Restoring a Catalog An Open File dialog will automatically take you to the DARWIN backups folder and list all available zipped archive files. Note: Both backups and exports have the same zipped archive structure and both may be present in this folder. You may change the folder if you have moved the backup or export archive to another location. Select the backup file from which to restore your catalog, and click Open. Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011

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