ECOCEAN Whale Shark Photo-identification Library Wiki

approving_an_encounter

2010-02-23T11:07:04-05:00

Field Manual: Approving or rejecting an encounter

The following steps describe how to approve or reject a newly submitted encounter for inclusion in the ECOCEAN Library. Sometimes encounters are added with incomplete or inaccurate information. It is best to leave these encounters as “Unapproved” until the submitter has been contacted and the information has been corrected.

Reviewing a new encounter

To review a new, unapproved encounter for inclusion in the library, follow these steps:

1. Look at the new encounter in the View Unapproved Encounters view (login required) and ensure that the its thumbnail image was correctly rendered. If not, use the Reset thumbnail command on the encounter page to choose a photo to render a new thumbnail from.

2. Check to make sure that all of the photos submitted contain material appropriate for display on the ECOCEAN web site. This is an important check to make sure that offensive material or photos showing inappropriate interaction with whale sharks are not displayed in the library. If the photos contain appropriate content and have enough information (scars, visible left- or right-side patterns in photos, or extractable spot patterns) to reasonably expect that the shark can be re-identified now or in the future, proceed to the next step. If the encounter contains offensive material, no photos, or poor quality photos, proceed to “Rejecting an Encounter” below.

3. Click on each photo one by one to view it in full detail. Note the presence of any distinguishing characteristics, such as scars, distinct spot patterning, or physical tags, using the pulldown list of keywords above each photo.

4. Check and edit the data submitted for each encounter as needed. For example, verify that the size estimate is realistic (30 feet versus 30 meters) and that the submitted comments contain appropriate language and good spelling.

5. Add the appropriate Location Code to the encounter and check any reported GPS coordinates for accuracy using the displayed Google Map.

6. If the content of the unapproved encounter is acceptable, click Approve to make the encounter visible to the general public once all of the above steps have been completed.

7. Check the TapirLink status of the encounter (true/false). The ECOCEAN Library TapirLink policy is available here.

Rejecting an encounter

There are two reasons to reject an encounter:

1. The encounter does not contain enough information to uniquely identify the shark now or in the future, but it does contain some useful data such as date and location, sex, size, etc. that can later be used for trending and aggregate analysis.

2. The encounter contains offensive or inappropriate content. These encounters should be deleted permanently.

To reject an encounter, click the Reject button in the left-hand blue bar of the encounter. This will give you two options:

a. Click Save as Unidentifiable to preserve this encounter but not make it available to the general public. Note: Unidentifiable encounters can be re-approved in the future if enough data is later submitted to allow for a reasonable chance of identification of this animal. As part of the Unidentifiable rejection process, an email is sent to the encounter submitter informing him/her of the unidentifiable status of the encounter and of the insufficiency of data needed for accurate identification. Some submitters may have additional photographs that can be added to each encounter to allow for approval and public display.

b. Click Permanently Delete to remove this encounter from the Library altogether. Note: Deleted encounters can be restored by a Library administrator. If you accidentally select Permanently Delete, email webmaster at whale shark dot org and reference the encounter number that you deleted to have the encounter restored.

Reaccepting an unidentifiable encounter

If you subsequently receive enough data for an unidentifiable encounter to allow for possible reidentification in the future, you can reaccept the encounter, moving it out of the unidentifiable status.

To reaccept an unidentifiable encounter, click Reaccept in the blue bar at the left of an unidentifiable encounter (a.k.a. a rejected encounter) to move it back to an Unapproved state.

Next: Extracting spot patterns
Previous: Managing encounters and sharks

Video

The following video demonstrates the concepts covered in this topic.

feature_requests

2010-01-21T02:14:21-05:00

Feature requests

Requests

The following features have been REQUESTED in the ECOCEAN Library:

Display locations associated with each potential match in the Modified Groth and I3S scan results
Let Interconnect determine the side being mapped rather than asking the user to choose ()i.e. use the positions of the reference spots to determine
Make the statistics page open to users, filtered by their appropriate location code
Bulk upload of photos, creating encounters automatically based on data extracted from the filename
Add an email submitter option for when an encounter cannot be identified

Completed

The following feature requests have been COMPLETED in the ECOCEAN Library:

Add an additional “Notify others” field for encounters - Marie Levine (SRI) and Simon Pierce (Marine Megafauna)
Add an optional alternate ID (i.e. local database identifier - David Rowat (MCSS)
Make Interconnect able to load I3S 2.0 FGP files - Simon Pierce (Marine Megafauna)

location_codes

2009-12-20T08:38:11-05:00

ECOCEAN Library Location Codes

The following are the location codes used for standardized location identification in the ECOCEAN Library.

1a - Ningaloo, non-specific

1a1 - North Ningaloo, off Exmouth

1a2 - South Ningaloo, off Coral Bay

1b - Christmas Island

1c - Indonesia

1d - Malaysia

1e - Thailand

1f - Myanmar

1g - India

2- Caribbean, non-specific

2a - Utila, Honduras

2b - Belize

2c - Mexico, East Coast

2d - Texas, Flower Gardens

2e - U.S. Gulf Coast

4a - Mozambique

4b - Tanzania

4c - Kenya

4d - South Africa permissions

4e- Djibouti

4f- Madagascar

4g - Red Sea

5a - Maldives

5b - Seychelles

6a - Donsol, Philippines

6b - Taiwan

7 - eastern Pacific

7a - Galapagos Islands

7b - Cocos Island

7c - Panama, Pacific coast

7d - Bahia de los Angeles, Mexico, Pacific

8a - Eastern Australian Coast

home

2009-10-27T23:12:57-05:00

Welcome to the ECOCEAN Whale Shark Photo-identification Library Wiki

This Wiki contains useful documentation for the ECOCEAN Library.

ECOCEAN Library User Documentation

The following documentation provides assistance to ECOCEAN Library users with login access.

Field Manual

1. Overview
2. Managing encounters and sharks
3. Approving or rejecting an encounter
4. Extracting spot patterns
5. Comparing spot patterns with sharkGrid
6. Interpreting pattern match results
7. Matching sharks
8. Searching through the Library
9. FAQs
10. Videos

Other topics
How to use Spot! for perspective correction
TapirLink, the GBIF, and the ECOCEAN Library
List of Photo Keywords (Tags)
List of Location Codes
Features, updates, and maintenance
Known Issues
Feature Requests

sharkGrid Documentation

How to Join sharkGrid

ECOCEAN Library Policies

ECOCEAN Library Access Policy
ECOCEAN Library Visitor Agreement
ECOCEAN Library User Agreement

known_issues

2009-09-04T12:47:45-05:00

Known Issues

The sharkGrid client has a slow memory leak. This will be fixed shortly.
Spot! exports all black, empty images on Linux systems…but not all.
The Encounter Calendar does not display in the Safari browser. A workaround is to use Firefox.

ecocean_library_access_policy

2009-06-09T14:15:49-05:00

ECOCEAN Whale Shark Photo-identification Library Access Policy

This policy defines who may be given access to the ECOCEAN Library and how access may be requested.

Background

The ECOCEAN Whale Shark Photo-identification Library (“ECOCEAN Library”) is privately funded and jointly managed by ECOCEAN, a non-profit organization in Australia, and ECOCEAN USA, a 501c3 non-profit organization in the United States. The ECOCEAN Library provides standardized research software and analytical techniques for the study of whale sharks (Rhincodon typus). Access to the ECOCEAN Library is provided free of charge to individuals or organizations selected according to the criteria of this policy. The number of new accounts that can be provided for the ECOCEAN Library each year is limited by:

ECOCEAN's available resources to support existing users
ECOCEAN's available resources for existing whale shark research efforts

Requesting access

Requests for access to the ECOCEAN Library should be sent via email to: webmaster at whaleshark dot org

In the request, please state:

Your research objectives
The organization you represent (if appropriate)
The timeframe of your research
How ECOCEAN Library tools and data could benefit your research
How much data you have already collected for your research
Your qualifications

Request review

Requests for access to the ECOCEAN Library are reviewed and voted upon by the Management Committee of ECOCEAN within 60 days. The Management Committee may also request outside assistance in reviewing your application.

The Management Committee weighs these and other criteria when reviewing a request for access:

Your ability and willingness to contribute new whale shark data
Your ability and willingness to follow the analytical techniques used in the ECOCEAN Library
Your ability and willingness to develop new techniques for whale shark research
Your ability and willingness to develop new science for other fields using whale shark data
Your ability and willingness to use whale shark data collaboratively
ECOCEAN's available resources to properly support you

The final decision for a request is made by a majority decision of the ECOCEAN Management Committee. Responses are provided via email. The Management Committee wishes to acknowledge in advance that not all valid requests for access can be approved due to limitations on available resources.

By invitation

The Management Committee of ECOCEAN may choose to invite appropriate individuals to participate in the ECOCEAN Library without a formal request for access. Invitations for access require a majority decision by the Management Committee and are reviewed in accordance with the criteria defined above.

how_to_join_sharkgrid

2009-03-16T01:29:46-05:00

How to Join sharkGrid

Welcome to the sharkGrid! The sharkGrid allows you to donate spare cycles of your computer to whale shark research. Specifically, the processing power of your computer can be “borrowed” for resource intensive tasks, such pattern recognition or data mining. sharkGrid uses “global volunteer computing” to distribute intensive tasks between multiple computers to allow them to complete much more quickly.

There are a few quick things you should know before participating in sharkGrid.

1. Once running, the sharkGrid client must stay open to allow your computer to aid in whale shark spot pattern processing. If for any reason you want to leave the grid, close the client. If you restart your computer, you must restart sharkGrid to participate.

2. Your Internet connection must remain open to participate in sharkGrid. sharkGrid obtains all patterns to compare from the World Wide Web.

3. Your computer must have a Java Runtime Environment (JRE) 5 or higher installed. You can download a JRE from the Sun Microsystems Java web site. The JRE is different from the Java Virtual Machine (JVM) that runs in your browser. The JRE allows Java applications to run as programs on your desktop.

4. Please disable any power saving features enabled on your computer. For example, many PCs will enter a suspended state (a.k.a. “System standby”) after a period of time with no user interaction. Other power saving schemes stop the hard drive(s), which will also interfere with the sharkGrid client.

5. sharkGrid participation is subject to the ECOCEAN Library Visitor Agreement. By visiting this web site and joining sharkGrid, you are agreeing to the terms and conditions therein.

6. sharkGrid can run in the background while you perform other tasks on your computer. However, sharkGrid is used for intensive computation, and other applications running on your computer simultaneously with sharkGrid may slow down.

7. sharkGrid requires significant computing power. We recommend you only run sharkGrid on computers with 1 gigabyte (GB) of RAM or more.

Downloading the sharkGrid client

You can download a zip file containing the sharkGrid client here.

Installing and starting the sharkGrid client

To install the sharkGrid client to your desktop, follow these instructions.

Figure 1. The sharkGrid client running successfully.

Windows

1. Unzip the sharkGrid client zip file to a custom folder on your Desktop or elsewhere on your computer. This is the folder that sharkGrid will run from.

2. Determine how much memory is available on your computer.

3. In the sharkGrid folder, right-click StartGridClient.bat and select Edit. This is the command-line statement used to start sharkGrid.

   java -classpath .;jdo2-api-2.0.jar;jpox-1.1.9.jar -Xms512m -Xmx1g workApplet3

You should edit ONLY the parameter ”-Xmx1g” to match the memory on your computer. You can specify your memory as megabytes (m) or gigabytes (g). The following are sample settings:

”-Xmx1g” or ”-Xmx1024m” for 1 gigabyte of RAM, which is also 1024 megabytes.
”-Xmx2g” or ”-Xmx2048m” for 2 gigabytes of RAM, which is also 2048 megabytes.

4. Save your changes to StartGridClient.bat.

5. Double-click StartGridClient.bat. You should see the sharkGrid client start and begin looking for work to do.

6. If the sharkGrid client fails to start, you may need to manually set the JAVA_HOME environment variable on your computer. This variable tells your computer where Java is installed so that it can use it when the “java” command is issued to start the sharkGrid client. Follow these steps on Windows to set JAVA_HOME:

 1. Right click on the My Computer icon on your desktop and select Properties.
 2. Click the Advanced Tab.
 3. Click the Environment Variables button.
 4. Under System Variables, click New.
 5. Enter the variable name as JAVA_HOME.
 6. Enter the variable value as the base directory of the JRE, such as C:\Program Files\Java\jre1.5.0_09. 
    The value you set depends on where the JRE was installed on your computer.
 7. Click OK.
 8. Double-click StartGridClient.bat. You should see the sharkGrid client start and begin looking for work to do.

Linux

1. Unzip the sharkGrid client zip file to a custom folder on your Desktop or elsewhere on your computer. This is the folder that sharkGrid will run from.

2. Determine how much memory is available on your computer.

3.This is the command-line statement used to start sharkGrid from the folder you unzipped it to.

   java -classpath .:jdo2-api-2.0.jar:jpox-1.1.9.jar -Xms512m -Xmx1g workApplet3

You should edit ONLY the parameter ”-Xmx1g” to match the memory on your computer. You can specify your memory as megabytes (m) or gigabytes (g). The following are sample settings:

”-Xmx1g” or ”-Xmx1024m” for 1 gigabyte of RAM, which is also 1024 megabytes.
”-Xmx2g” or ”-Xmx2048m” for 2 gigabytes of RAM, which is also 2048 megabytes.

This command assumes that Java 5 or higher is already installed and available from the command line. Click here for instructions for installing Java on Linux.

4. Create a shell script containing this command and consider creating a cron job to run this script during the times of the day that you know your machine will be idle.

Mac

TBD