Workshop at the18 th Biennial Conference on the Biology of Marine Mammals

1. Workshop at the18th 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/18thBiennialWorkshop.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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

3. Software overview • DARWIN is a software system that: • provides access to a collection of digital dorsal • fin images along with textual information • allows users to query a database of • previously identified dolphin dorsal fin images • with a new sighting image of a dolphin's fin • allows users to query the system with the name • of a specific individual • allows users to sort and view a collection of • images based upon sighting location, sighting • date, or damage category. Workshop at the18th Biennial Conference on the Biology of Marine Mammals – October 2009

4. Software installation • Insert the CD • Double-click darwin-2.02-setup.exe • A dialog should appear as at left. Check the box to accept the license agreement • Click “Next” 5. The default directory for installation is shown 6. To specify a different installation directory, click “browse” and navigate to the desired directory. After clicking OK, the selected directory should appear with “darwin-2.0” appended to the end. It is recommended that you do not delete “darwin-2.0” from the end of the path. 7. Click “Install” Workshop at the18th Biennial Conference on the Biology of Marine Mammals – October 2009

5. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

6. Creating Your Own Catalog Scheme To create your own catalog scheme, select “Define New Scheme” from the “Settings-> Catalog Scheme” menu Workshop at the18th Biennial Conference on the Biology of Marine Mammals – October 2009

7. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

8. Using a Custom Catalog Scheme Once you have created a new scheme, that scheme will not become active until you select it. (And once a catalog has been created with one scheme it cannot be converted to another) To activate your own catalog scheme, select “Select Active” from the “Settings-> Catalog Scheme” menu Workshop at the18th Biennial Conference on the Biology of Marine Mammals – October 2009

9. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

10. 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 ending in .db • 6. Hit “OK” Workshop at the18th Biennial Conference on the Biology of Marine Mammals – October 2009

11. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

12. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

13. 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” stage 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 must 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

14. Tracing a fin outline • Once the “Trace outline” button has been clicked, the program transitions to the tracing stage with the trace window enabled to trace a fin outline. • Click at a point on the leading edge of the fin, then click on 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 • If no modifications to the outline are desired, the user may simply click on the “Locate Features" button. Workshop at the18th Biennial Conference on the Biology of Marine Mammals – October 2009

15. 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 on the “Add to Database” button. You do not need to click on 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

16. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

17. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

18. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

19. Tracing Difficulties: hi-contrast waves • Trace the fin as previously described. • 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

20. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

21. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

22. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

23. Importing a Catalog From the Main Window FILE/Import menu select Import Catalog Workshop at the18th Biennial Conference on the Biology of Marine Mammals – October 2009

24. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

25. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

26. Opening a different catalog To open an existing catalog from a folder of your choosing, select “Open Database” from the File menu. Workshop at the18th Biennial Conference on the Biology of Marine Mammals – October 2009

27. Opening a different catalog The current path is shown at the top of the dialog. Navigate to the correct folder. Select the .db file to open. Click the “Open” button. Workshop at the18th Biennial Conference on the Biology of Marine Mammals – October 2009

28. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

29. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

30. 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 move it to its proper location. Workshop at the18th Biennial Conference on the Biology of Marine Mammals – October 2009

31. Matching a fin against the catalog After tracing the fin, click on the “Match” button in the trace window. A dialog will appear as shown at left. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

32. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

33. 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 The user may close the window by clicking Done Workshop at the18th Biennial Conference on the Biology of Marine Mammals – October 2009

34. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

35. 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 point to indicate the likely position of the occluded edge Workshop at the18th Biennial Conference on the Biology of Marine Mammals – October 2009

36. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

37. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

38. Matching Difficulties: long leading edge When a leading edge is elongated by the view or dolphins movement, it may be advantageous to tend toward a shorter trace. Workshop at the18th Biennial Conference on the Biology of Marine Mammals – October 2009

39. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

40. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

41. The Matching Queue A list of the names of previously saved fin files may be created using ... Add and Remove Workshop at the18th Biennial Conference on the Biology of Marine Mammals – October 2009

42. The Matching Queue Matching queue include 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

43. 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 click 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

44. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

45. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

46. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

47. Restoring a Catalog From the Main Window FILE menu select Restore Workshop at the18th Biennial Conference on the Biology of Marine Mammals – October 2009

48. 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 the18th Biennial Conference on the Biology of Marine Mammals – October 2009

49. Restoring a Catalog Click OK if ready to proceed, and restore will recreate any missing or damaged file structure and catalog contents, including ... the survey area folder and its subfolders the catalog database and all image files You will be prompted if conversion from a previous DARWIN catalog format is necessary. Workshop at the18th Biennial Conference on the Biology of Marine Mammals – October 2009

50. Exporting a Catalog From the Main Window FILE/Export menu select Export Catalog Workshop at the18th Biennial Conference on the Biology of Marine Mammals – October 2009