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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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Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

Restoring a Catalog

From the Main Window FILE menu select Restore

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

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


Workshop at the19 th biennial conference on the biology of marine mammals

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 the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Exporting a Catalog

From the Main Window FILE/Export menu select Export Catalog

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Exporting a Catalog

In the Save File dialog select a folder and enter a filename for the zipped archive file, and then click Save

The export archive will contain ...

the catalog database file (*.db)

all images related to the catalog

The export archive does not contain ...

saved fin traces in the same survey area

saved match results related to the catalog

(There is no difference between a backup archive and an export archive, except that you are allowed to specify name and location of the export file.)

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Exporting Fins from the Catalog

From the Main Window FILE/Export menu select Export Fin (*.finz)

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Exporting Fins from the Catalog

A list of all fins in the current catalog will appear.

Select one or more fins in the list (shift-click for ranges and ctrl-click for individuals) and click Save Fin(s)

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Exporting Fins from the Catalog

In the Save File dialog select or create a folder (tracedFins is the default) within which to save the FINZ files. Then click Save.

Each FINZ file will be named using the dolphin ID and a subscript as necessary.

Examples: echo.finz, echo[2].finz

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Opening a Saved / Exported Fin

From the Main Window FILE menu select Open Fin or click the Open button (with the fin silhouette)

From Microsoft Windows Explorer ...

double-click on a FINZ file or ...

right-click and select Open with darwin, and the Trace Window will open and display the fin image and traced outline.

The trace of a previously saved fin is “locked” and can only be modified by reloading the original image and tracing the fin outline from the beginning

If the fin is opened from the Main Window, it can be matched to the catalog, but if the fin is opened from Microsoft Explorer, it can only be viewed

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Importing Fins into a Catalog

From the Main Window FILE menu select Import Fin (*.finz)

Any previously saved fin or collection of fins from any location can be imported into the currently open catalog

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Importing Fins into a Catalog

From the Select Fin dialog choose the location and fin files to be imported into the current catalog and click Open

Any fin traces that have damage categories that are not defined in the current catalog’s category scheme will be reassigned the category “Undefined”

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Exporting Full-size Fin Images

Since version 1.85, DARWIN has saved only thumbnails of images modified during fin tracing.

These PNG image files contain the name of the original image and a list of all modifications made using DARWIN. Full-size images are rebuilt from originals by reapplying these modifications any time DARWIN loads a fin.

You can export full-size modified images from DARWIN for use elsewhere.

From the Main Window FILE/Export menu select Export Images (full-size)

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Exporting Full-size Fin Images

Select a fin or fins from the displayed list and click Save Image(s)

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Exporting Full-size Fin Images

Then select or create a folder and click Save

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Exporting Sighting Data

From the Main Window FILE/Export menu select Export Sighting Data

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Exporting Sighting Data

Check boxes allow you to select which sighting data fields to export, then click OK.

A Save File dialog allows you to enter a file name for the exported data and Save it

Data is saved in a tab-separated text file format suitable for import into most spreadsheets (including Excel, SOCPROG, ...)

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

DARWIN on an external hard drive

DARWIN can be installed on an external drive (hard drive, thumb-drive, whatever)

However, DARWIN always attempts to load the last used catalog when it is started. If the drive letter has changed when the external drive is moved from one computer to another, then DARWIN will fail to load the last used catalog.

To recover, from the Main Window FILE menu select Open Database, locate the catalog file (for example, myCatalog.db) and click the Open button

Then use DARWIN normally

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Where is everything on a PC?

The DARWIN application folder hierarchy is …

darwin-2.0

system

bin, lib, etc(system folders)

darwin.cfg (configuration file)

surveyAreas (v2.02 and earlier)

sample

(catalogs, sightings, tracedFins, …)

backups (backup/export archives)

docs(help files)

licenses-etc (legalese)

In DARWIN versions 2.02 and earlier the DATA folders were all within the application folder hierarchy. Now they may be anywhere.

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Where is everything on a PC?

The DARWIN data folder hierarchy is …

darwinPhotoIdData

surveyAreas

TampaBay (one of possibly many)

catalog (catalog files)

tracedFins (saved traces)

matchQueues (saved fin queues)

matchQResults(saved match results)

sightings (exported sighting data)

backups (backup/export archives)

Data folder collections may be placed anywhere, as long as they are within a folder named darwinPhotoIdData

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Where is everything on a Mac?

The DARWIN application folder hierarchy is …

darwinMac.app/Content/MacOs

system

bin, lib, etc(system folders)

.darwinrc (configuration file)

surveyAreas

sample

(catalogs, sightings, tracedFins, …)

backups (backup/export archives)

docs(help files)

licenses-etc (legalese)

In all darwinMac versions the DATA folders may be placed anywhere.

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Where is everything on a Mac?

The DARWIN data folder hierarchy is …

darwinPhotoIdData

surveyAreas

TampaBay (one of possibly many)

catalog (catalog files)

tracedFins (saved traces)

matchQueues (saved fin queues)

matchQResults(saved match results)

sightings (exported sighting data)

backups (backup/export archives)

Data folder collections may be placed anywhere, as long as they are within a folder named darwinPhotoIdData

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Vista & Windows 7 – Where is my data?

Microsoft Vista and Windows 7 manage user data files and profiles differently than Windows XP

DARWIN is no longer installed in the “Program Files\darwin2.0” location by default. If it is in this location on a Vista of Windows 7 computer, the catalogs, fin traces, modified images, match results, etc will actually be placed in hidden AppData/local or AppData/roaming user files

DARWIN can sometimes find them, but not always. So …

We really recommend that DARWIN be installed outside of the Program Files folder. This prevents all issues related to inadequate permissions and apparent loss of image files when viewing an existing catalog.

The new default location for installing DARWIN is this. We recommend something similar in all cases.

C:\darwinPhotoId\darwin-2.0

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Vista & Windows 7 – Where is my data?

If you have installed DARWIN in the default “C:\Program Files\darwin2.0” location on a Vista or Windows 7 machine, and if you need to find the “missing” files MANUALLY, you must …

First make sure you can see hidden files and folders.

Open the Control Panel, click Appearance and Personalization, click Folder Options, click the View tab, scroll down and click the radio button labeled Show hidden files and folders, and finally click OK

Now you can use Windows Explorer to navigate to one of these locations to find your files …

C:\Users\<username>\AppData\Local\darwin-2.0\...

(if you installed DARWIN on a stand alone computer or one in a non-domain based network or a network without roaming profiles)

C:\Users\<username>\AppData\Roaming\darwin-2.0\...

(if you installed DARWIN on a computer with roaming profiles on a domain-based network)

NOTE: <username> may be your username or “All Users”

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

What is in the Catalog?

A catalog is a set of files located in the catalog folder within some survey area. Multiple catalogs may exist in this same folder.

Each catalog has an SQL database file containing fin traces, names of image files and sighting data. All image files (modified and original) are stored alongside the database file

A typical small catalog of 2 fins might contain …

TampaBay.db

2sla.jpg2sla_wDarwinMods.png

PAPI.bmpPAPI_wDarwinMods.ppm

(1) Modified files may be either thumbnail PNG or full-size PPM images, depending on the DARWIN version.

(2) You should NEVER manually rename image files in the catalog folder.

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

How can I clean up my catalog?

Since DARWIN mixes files for multiple catalogs in the same survey area, you may reach a point where you want to separate them

Do this with these simple steps.

Open and then Export each catalog to a separate export archive. Make sure to export them ALL.

Then, Import each catalog into a new survey area (a different one for each catalog).

Any previously saved fin traces you want to move to the new survey area will have to be manually copied

When you are ABSOLUTELY sure that the new versions of each catalog are intact and error free, then AND ONLY THEN consider manually deleting the OLD survey area

surveyAreas (before)

default

workshop.db

myCatalog.db

… images …

surveyAreas (after)

workshop

workshop.db

… images …

mySurvey2009

myCatalog.db

… images …

default

workshop.db

myCatalog.db

… images …

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

Converting a non-SQL Database?

DARWIN 2.0+ uses an SQL database file format

Earlier versions of DARWIN used a different format

The Open Catalog,Import and Restore operations may detect that a database format conversion is necessary

In the What to backup dialog …

Select both options if you initiated this with an Open Catalog request (this will ensure a complete backup of the existing catalog before continuing)

Select neither option If you initiated this with an Import or Restore request

Click OK and the catalog will be converted to the SQL format and the Open Catalog, Restore or Import will complete

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


Workshop at the19 th biennial conference on the biology of marine mammals

What is in the Configuration file?

The configuration file - darwin.cfg (PC) or .darwinrc (Mac) - contains …

Paths to installed HOME folder, current data path, survey area and last opened catalog

Parameters for active contour, fonts, colors, etc

All defined catalog schemes

Names of all survey areas and catalogs

Workshop at the19th Biennial Conference on the Biology of Marine Mammals – November 2011


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