VARS: Annotation

This guide gives basic instructions for starting and using the VARS annotation interface. Useful definitions and descriptions can be found in the Glossary below. If you need extra help or information, please contact us.

Getting started

1. 1. Start the program by double-clicking on the varsannotation.jnl
   2. The VARS logo will appear while the knowledge base loads and the annotation app starts up. This may take a minute or so.
   3. To begin using VARS you must first login, connect to the VCR, and open the tape set that you wish to annotate.
      For user login, type in your username and your password (or type ‘guest’).

      

      If you have not created a user account previously, select the Create a new user account. In the Create new user window choose an appropriate user login name and password. Also fill in your personal details including affiliations/organization. Once completed, select OK. Note: Do NOT use your network or any other secure password as it will be viewable by the VARS administrators.

      

   4. VARS gets tape timecode and VCR deck control through RS-422 protocol. To connect to the VCR, click the VCR button and in the window that opens, select the following:

      When in the lab: RS422 as the timecode source and choose /dev/tty.RS422 deck control under the RS422 port selector.

      When at sea: ‘Select timecode source’ should be set to UDP and server host and port numbers should already be entered and you should not need to alter these settings.

      

The interface screen now appears as below, note that the user and video connection boxes should now appear as green checks instead of red X’s.

Annotation mode: At the lower left of the VARS annotation screen, choose an annotation mode (style of annotation). The default mode is Outline mode and is used for at-sea annotations.

Camera direction: At lower right of screen describes the direction of ROV travel. The default direction is descend, but the direction should be updated as ROV direction changes throughout the dive.

Adding and modifying annotations

These are basic directions for creating and modifying annotations. Definitions or descriptions of the various parts of the interface can be found in the Glossary below. Some keyboard shortcuts are included in the instructions. NOTE: We use the terms observation and annotation interchangeably in the documentation below.

Adding an annotation

1. Click on the New button (or ctrl+N / cmd+N). A new annotation line will be created in the observation table with the default object in the observation column and with the current video VCR timecode.
2. Type the concept name in the editor and press Enter. The new concept name will be updated in the observation table.
3. 

Adding an annotation with a frame grab

1. To create an annotation associated with a frame grab, click the frame grab (F) button (or ctrl+F/ cmd+F ).The frame grab will be displayed in the upper right corner of the user interface, under the Frame-grab tab. By default, the concept physical-object will be entered in the observation column. The F button in the FG/S column of the observation table will be highlighted in green, indicating there is a frame grab associated with this observation
2. 
3. To give the annotation a more specific name (concept), type the concept in the concept editor (located just under the observation table), and press Enter.

Duplicating an observation

1. 1. Click on the row with the observation to be copied.
   2. Click on the green Copy Anno button (or press cntrl + G on the keyboard). This will duplicate the observation and its associations to a new row with a new time code.

Creating multiple observations for a single time code

1. To create multiple observations with the same time code, click the row with the desired time code.
2. Select the Copy TC button (or press Cntrl + D on the keyboard). Rename the duplicate timecode observations as appropriate.
   

   

Adding an association to an observation

An association is a structured descriptor that provides additional information about an annotation. For example, color of the item, behavior such as swimming or eating, resting on some substrate, etc.

1. Add an association by selecting a row in the annotation table.
2. In the concept editor click on the green + button.
3. In the association search box, type part of the association you wish to search for and press Enter. You can continue to press Enter to scroll through additional matches.
4. Press the green + button again to add the association. (The association editor will automatically close.)
5. 

Adding an association using the blue ‘Quick annotation association’ buttons

1. 1. Click on the blue annotation button that represents the association you wish to add. The choices are:
      S (sample)
      N (population)
      ? (identity uncertain)
      C (close-up)
      New# (new reference number)
      Old# (old reference number)
      Good (good image quality)
      D (dense population).
      See buttons in the annotation glossary, for details.

Deleting an observation

1. 1. Highlight the observation line to be deleted.
   2. Click the red Delete button. The row will be deleted from the table (with a warning). Multiple lines can also be selected and deleted.

NOTE: VARS has undo/redo buttons on the toolbar in case you delete observations you meant to keep. You can undo the last 25 operations in VARS.

Deleting an association from an observation

1. 1. Highlight the observation row to be edited, so that the associations for that observation will appear in the concept editor.
   2. In the concept editor, highlight the association to be deleted.
   3. Click the red X (Remove Association) button and the association will disappear from the concept editor or the observation table.

Custom icon tabs

If you do a lot of annotations, setting up a custom icon tab (in the panel area across the bottom of the interface) allows adding new observations quickly. For this panel, each icon is really a word—specifically the name of a concept. For efficient annotation, you can create separate tabs for different types of dives, such as Geology or Midwater, and populate each with the names of commonly observed objects in those categories.

Creating custom icon tabs

If you do a lot of annotations, setting up a custom icon tab (in the panel area across the bottom of the interface) allows adding new observations quickly. For this panel, each icon is really a word—specifically the name of a concept. For efficient annotation, you can create separate tabs for different types of dives, such as Geology or Midwater, and populate each with the names of commonly observed objects in those categories.

1. To create an icon tab, click on the New (green +) button at the right of the icon panel. At the prompt, name the new tab.
   
2. In the concept edit window search box, type the name of the object that you would like to add to the tab.
3. Press Enter until the correct object is highlighted.
4. Click on the name, and drag it onto the tab that you created. The name is now an icon.
   
5. Continue adding icons as needed.
6. Organize the icons by dragging them around within the tabs.
7. To delete an icon (concept) from a tab, right-click on the icon, and select Delete from the drop-down menu.
8. To locate a concept in an icon tab within the knowledge base tree (for reference), right-click on the icon in the panel, and select Find in knowledgebase tree from the drop-down menu. The concept will be highlighted in its correct position in the knowledge base.

Adding observations using icons

1. Click on the icon with the name of the concept to be added. The observation will be added to the table along with the current VCR time code.
2. Add associations as necessary using the Associations buttons or association editor.

Getting started

1. 1. Start the program by double-clicking on the varsannotation-video.jnlp.
   2. The VARS logo will appear while the knowledge base loads and the annotation app starts up. This may take a minute or so.
      After the knowledgebase finishes loading, the annotation interface opens.
   3. To begin using VARS for video files, you must first login, then open the video file that you wish to annotate.
      For user login, type in your username and your password (or type ‘guest’).

      If you have not created a user account previously, select the Create a new user account. In the Create new user window choose an appropriate user login name and password. Also fill in your personal details including affiliations/organization. Once completed, select OK. Note: Do NOT use your network or any other secure password as it will be viewable by the VARS administrators.

      

   4. Select the video button to open and existing or new video file. Within the new window that opens, do the following:
      • To open new video files select open by location, browse to and select the video file you wish to annotate and choose open then select the ROV name from the camera platform drop-down menu and enter the dive number into the sequence number box.
      • To open a previously annotated video file, choose open existing and select the name of the file you wish to re-open. Select a timecode source, choices include automatic, timecode track, or elapsed depending upon needs and file source. Press OK.

The interface screen now appears as below, note that the user and video connection boxes should now appear as green checks instead of red X’s.

Under video player, you may choose to play videos using the built in player or the Quicktime component. The video player you select will depend upon the video container and codec that you are using.

Annotation mode: At the lower left of the VARS annotation screen, choose an annotation mode (style of annotation). The default mode is Outline mode and is used for at-sea annotations.

Camera direction: At lower right of screen describes the direction of ROV travel. The default direction is descend, but the direction should be updated as ROV direction changes throughout the dive.

Adding and modifying annotations

These are basic directions for creating and modifying annotations. Definitions or descriptions of the various parts of the interface can be found in the Glossary. Some keyboard shortcuts are included in the instructions. NOTE: We use the terms observation and annotation interchangeably in the documentation below.

Adding an annotation

1. Click on the New button (or ctrl+N / cmd+N). A new line will be created in the observation table with the default object in the observation column and with the current video file timecode.
2. Type the concept name in the editor and press Enter. The new concept name will be updated in the observation table. For faster annotations see information below about a custom icon panel.

Adding an annotation with a frame grab

1. To create an annotation associated with a frame grab, click the frame grab (F) button (or ctrl+F/ cmd+F ). The frame grab will be displayed in the upper right corner of the user interface, under the Frame-grab tab. By default, the concept physical-object will be entered in the observation column. The F button in the FG/S column of the observation table will be highlighted in green, indicating there is a frame grab associated with this observation.
2. To give the annotation a more specific name (concept), type the concept in the concept editor (located just under the observation table), and press Enter.

Duplicating an observation

1. 1. Click on the row with the observation to be copied.
   2. Click on the green Copy Anno button (or press cntrl + G on the keyboard). This will duplicate the observation and its associations to a new row with a new time code.

Creating multiple observations for a single time code

1. To create multiple observations with the same time code, click the row with the desired time code.
2. Select the Copy TC button (or press Cntrl + D on the keyboard). Rename the duplicate timecode observations as appropriate.
   

   

Adding an association to an observation

An association is a structured descriptor that provides additional information about an annotation. For example, color of the item, behavior such as swimming or eating, resting on some substrate, etc.

1. Add an association by selecting a row in the annotation table.
2. In the concept editor click on the green + button.
3. In the association search box, type part of the association you wish to search for and press Enter. You can continue to press Enter to scroll through additional matches.
4. Press the green + button again to add the association. (The association editor will automatically close.)

Adding an association using the blue ‘Quick annotation association’ buttons

1. 1. Click on the blue annotation button that represents the association you wish to add. The choices are:
      S (sample)
      N (population)
      ? (identity uncertain)
      C (close-up)
      New# (new reference number)
      Old# (old reference number)
      Good (good image quality)
      D (dense population).
      See buttons in the annotation glossary, for details.

Deleting an observation

1. 1. Highlight the observation line to be deleted.
   2. Click the red Delete button. The row will be deleted from the table (with a warning). Multiple lines can also be selected and deleted.

NOTE: VARS has undo/redo buttons on the toolbar in case you delete observations you meant to keep. You can undo the last 25 operations in VARS.

Deleting an association from an observation

1. 1. Highlight the observation row to be edited, so that the associations for that observation will appear in the concept editor.
   2. In the concept editor, highlight the association to be deleted.
   3. Click the red X (Remove Association) button and the association will disappear from the concept editor or the observation table.

Custom icon tabs

If you do a lot of annotations, setting up a custom icon tab (in the panel area across the bottom of the interface) allows adding new observations quickly. For this panel, each icon is really a word—specifically the name of a concept. For efficient annotation, you can create separate tabs for different types of dives, such as Geology or Midwater, and populate each with the names of commonly observed objects in those categories.

Creating custom icon tabs

If you do a lot of annotations, setting up a custom icon tab (in the panel area across the bottom of the interface) allows adding new observations quickly. For this panel, each icon is really a word—specifically the name of a concept. For efficient annotation, you can create separate tabs for different types of dives, such as Geology or Midwater, and populate each with the names of commonly observed objects in those categories.

1. To create an icon tab, click on the New (green +) button at the right of the icon panel. At the prompt, name the new tab.
   
2. In the concept edit window search box, type the name of the object that you would like to add to the tab.
3. Press Enter until the correct object is highlighted.
4. Click on the name, and drag it onto the tab that you created. The name is now an icon.
   
5. Continue adding icons as needed.
6. Organize the icons by dragging them around within the tabs.
7. To delete an icon (concept) from a tab, right-click on the icon, and select Delete from the drop-down menu.
8. To locate a concept in an icon tab within the knowledge base tree (for reference), right-click on the icon in the panel, and select Find in knowledgebase tree from the drop-down menu. The concept will be highlighted in its correct position in the knowledge base.

Adding observations using icons

1. Click on the icon with the name of the concept to be added. The observation will be added to the table along with the current VCR time code.
2. Add associations as necessary using the Associations buttons or association editor.

This is a list of the various entry items and buttons on the VARS Annotation interface. Details on how to use these features are in the VARS Annotation User Guide.

Definitions and descriptions

The type of item and/or the window where it appears is noted in parentheses.

? (annotation button)
Use to indicate that the identity is uncertain.

Annotation Mode (main window, bottom left)
Select the mode—Outline or Detail.

Outline annotations include animals discernible at approximately 2x real-time tape speed. The level (species, genus, family, etc.) and certainty of identification depends on current knowledge of deep-sea organisms and physical factors, such as ROV speed, camera setting, or visibility. Outline annotation also includes characterization of major habitats, such as seep or canyon wall, and geological features such as rock outcrop, sand, or fault. The characterization is usually annotated at a regular intervals (approximately five minutes), at identification of samples and equipment, and at the start and end of transects.

Detailed annotations include all discernible organisms, behaviors, and habitats possible at real-time speed.

association
Descriptor(s) for physical object in observation. The descriptor must match an association entered in the knowledge base, or it will not be recognized by VARS.

buttonsThe buttons in the middle of the interface have various purposes. Some are action buttons and some are annotation buttons.

• action buttons (green or red):
  New, Copy TC, Copy Anno, F, and Delete.
  (Note: Delete is not always visible.)
• annotation buttons (blue):
  S, N, ?, C, New#. Old#, Good, and D.

C (double C button)Indicates a close-up view.

Camera Data tab

• Direction
  Choose the direction that the ROV is moving (launch, descend, cruise, stationary, starttransect, transect, endtransect, ascend). Default value when starting a new video set is descend.
• Name
  Enter the name of the camera that recorded the observation—Ventana or Tiburon.
• Zoom
  Displays the value to which the camera is currently zoomed.
• Focus
  Displays the value to which the camera is focused.
• Iris
  Displays the setting for the aperture (iris), which controls the light and depth of field.
• FieldWidth
  This is the width of the field visible in the frame and varies with the Zoom value.
• StlllImage
  Displays the directory in which the frame grab (still image) is stored.

columns See Observation Table Columns
concept Name of physical object in observation. Must match a concept entered in the knowledge base or will not be recognized by VARS.
Connect (File>Connect)  File menu option that allows the user to log in to the VARS database and to connect to the video recorder through the VARS interface (VCR control feature is read-only aboard the ships). User must choose COM1 or COM2 (usually COM1) and specify VCR type (default is Sony).
Custom (concept) icon tab

A user’s custom panel of one-click icon buttons for most commonly-used concepts, located at the bottom of the interface with the user ID on a tab.. To create a custom panel, see the detailed instructions in the User Guide

• New tab
  Add a new concept icon tab
• Remove
  Remove a concept icon tab

Copy Anno (button) Creates a new row in the observation table with the same
concept (and associations) as the highlighted row but a new time code.
Copy TC (button)Creates a new row in the observation table with the same time code and concept as the highlighted row. You can then change the concept. Useful for situations with more than one object in a frame (grab).
D (button) Population quantity dense
Delete (button) Delete observation row.
Edit

Drop-down menu with these selections:

• Reload Knowledge Base
• Update with info from camera-logs and EXPD
  Select this to link the camera log and ROV nav data to the annotations after annotating an archive set.

Exit File menu option. Quits the program.
F (button) Creates a new row in the observation table with physical-object’concept and a frame grab. A green F will appear in the FG/S column for that observation.
File A drop-down menu with three options: Connect, Open Archive, and Exit
Frame-grab tab Displays a frame grab of the observation that is highlighted, if it is available.
Good (button) Image quality is good. green checkmarks (bottom of the screen)Displays the current user name (should be updated as annotator changes), the status of connections to the VCR and the VARS database, and the video archive currently in use (camera platform, dive number, and tape number).
Help (Coming soon)
User support documentation.
About and Version information
keyboard shortcuts The following shortcuts may be used, instead of clicking buttons, to create new or multiple annotations. (Using keyboard shortcuts reduces the risk of repetitive strain injury from excessive mouse clicking.)
Ctrl + n = New: Create a new observation
Ctrl + d = Copy TC: Create a new observation with a selected timecode
Ctrl + f = Copy Anno: Copy an observation to a new timecode

knowledge base A dictionary of objects referenced by the annotation interface and the VARS query to maintain the entry of consistent annotations. The doctionary covers the enormous variety of animate and inanimate objects commonly (or rarely) observed in Monterey Bay and other regions by MBARI ROVs.
Some of the main categories are Behavior, Ocean-zone, and Physical-object. Physical object—the largest category—includes marine organisms, biological structure, behavior, geological features, and equipment attached to or deployed by ROVs. Miscellany (under Physical-object) includes items not covered by the other categories, such as equipment attached to the ROVs or deployed by the ROVs during research missions. It even specifies several categories of trash. Annotators can use all of these items to describe an organism, geological feature, or piece of equipment in detail.

Knowledge Base tab Displays the entire knowledge base as a searchable tree so users can navigate through the hierarchy and view the parents and children of a concept of interest.
N (button) Population quantity 999 (3 or more individual objects observed in a frame)
New (button) Creates a new row in the observation table with the  object concept.
New # (button) Adds a new identity reference to the observation (auto-increments throughout annotation session)
Observation tab

• TimeCode
• Concept
• RecordedDate
• ObservationDate
• Observer

Observation table columns

The observation table is the large area in the upper left of the window. The various columns are:

• Time Code 
  Digital Betacam video record time at which the observation occurred.
• Concept
  The concept name of the object that was observed.
• Association
  Contains associations describing an observation.
• FG/S
  The F button is green when a frame grab is associated with the observation. The S button is blue when a sample is associated.
• Observer
  Displays the user name that was logged in when annotations were created.
• Camera Direction 
  Displays the ROV direction (ascend, descend, etc.) for each line of annotation.
• Tape ID
  Displays the camera platform, dive number, and tape number for each line of annotation. Example: T684-01 means  Tiburon dive #684, Tape 01.
• Notes
  Displays any notes added to a line of annotation.

Old # Allows you to choose a previously assigned identity reference for an observation
Open Archive Allows user to select the camera platform (e.g, Tiburon or Ventana), dive number and tape number they wish to annotate or edit. If tape has been previously annotated, those annotations will appear in the observation table.
Physical Data tab

• Latitude
• Longitude
• Depth
• Temperature
• Salinity
• Oxygen
• Light

Reload KnowledgeBase Edit menu item. Select to update to the most current version of the Knowledge base (e.g., just after a new concept has been added).
S (button)Sample. A blue S will appear in the FG/S column for that observation.
Update with info from camera-logs and EXPD See Edit definition. Select this at the end of annotating an archive set to link the camera log and ROV nav data to your annotations.
VCR control panel The interface includes a VCR control panel for use in onshore annotation. The controls are identified below.
NOTE: These controls are NOT usable on the ships.

View (menu bar, top)A drop down menu with one selection, Video Set, which opens another window, showing the annotations from all the tapes in the current tape set.
Video Archive tab

• redcordedDate
• videoArchiveName
• shipName
• platformName
• formatCode
• startDate
• endDate
• chiefScientist
  Displays the name of the chief scientist of the expedition.
• diveNumber
• trackingNumber

Video Set  (View>Video Set) See View.