Annotation and Scenes Best Practices

Annotations and Scenes Best Practices

Summary

1. Verify data files are in a common directory tree and file names are reasonable.
2. If a multi-tab scene will be created, enter Tile Tabs (View Menu->Enter Tile Tabs).
3. Adjust size of window.
4. Setup view of the models (pan/rotate/zoom).
5. Lock Aspect Ratio (click Lock Aspect button in right side of Toolbar).
6. Enter Annotations Mode (click Annotate button in Toolbar).
7. Add Annotations.
8. Display the Scene Dialog (click Clapboard icon in Toolbar or select Window Menu->Scenes) and add a Scene (click Add button on Scene Dialog).
9. Save the Scene File. Click Save As button the first time to set the path and name of the scene file. Once path and name of scene file has been set, use the Save button.
10. Repeat last few steps to edit annotations and create additional scenes.
11. Be sure to save the Scene File (click Save button or Save As if Save is disabled at top of Scene Dialog).

Introduction

Describing annotations and scenes is best done using an analogy with Microsoft PowerPoint. PowerPoint allows one to create a presentation consisting of slides saved into a PowerPoint file. These slides are annotated with text and various shapes. In wb_view, a scene is analogous to a PowerPoint slide and a Scene File contains multiple scenes just like a PowerPoint file contains multiple slides. In wb_view, one annotates a scene similar to the way one annotates a slide in PowerPoint. A Scene saves ‘the state’ of wb_view so that when the scene is loaded at a later time, by either the creator of the scene or another user, the user-interface and the orientation of the brain models replicates ‘the state’ at the time the scene was created.

When creating scenes and annotations, following a set of “best practices” ensures that one efficiently creates scenes that are properly displayed at a later time and when shared with other users.

Best Practices Details

1. Verify data files are in a common directory tree and file names are reasonable. Scenes contain the directory path and filename for each data file that is loaded at the time the scene is created. Once a scene has been created, moving or renaming a data file referenced by the scene will cause an error when the scene is displayed. In addition, if data files are scattered about many directories, this may cause problems when zipping a scene file and its data files or uploading a scene file to the BALSA database.

2. If a multi-tab scene will be created, enter Tile Tabs (View Menu->Enter Tile Tabs). Tile Tabs displays all of the window's tabs in a grid pattern. The number of row and columns in the Tile Tabs view is edited on the Tile Tabs Configuration Dialog (View Menu->Tile Tabs Configuration->Create and Edit). Advanced parameters include “stretch factors” that allow one to increase the size of a row or column relative to other rows and columns. One may also save the configuration for future use. If a scene is created, the configuration is added to the scene so that the configuration is available when the scene is displayed.

3. Adjust size of window. It is important to adust the size of the window prior to entering Annotations Mode (further down in this list).

4. Setup view of the models. Pan (drag mouse with SHIFT key down), Rotate (drag mouse), Zoom (drag mouse with Control Key. Use the Command Key on Mac.

5. Lock Aspect Ratio (click Lock Aspect button in right side of Toolbar). As a general rule, once the aspect ratio is locked, it should remain locked. The aspect ratio is the ratio of height divided by width. Annotations in tab and window spaces are positioned using percentage coordinates that range from 0% to 100% with 0% at the left (x) and bottom (y) and 100% at the right (x) and top (y). If the window is resized with the aspect ratio unlocked and there is a change in the aspect ratio, annotations in tab/window space may no longer appear in the correct location (such as over an anatomical feature). Locking the aspect ratio adds padding to the left and right or bottom and top of the graphics region so that the model’s region maintains the same aspect ratio (ratio of height to width). This ensures that annotations remain in the correct location relative to the viewed brain model.

6. Enter Annotations Mode (click Annotate button in Toolbar).

7. To add annotations, click any of the Space and/or Type icons in the Insert New section of the Annotation Toolbar and then click in graphics region to create the annotation. A new annotation is automatically selected so that it can be moved/resized with the mouse or its attributes changed using controls in the toolbar.

8. Display the Scene Dialog (click Clapboard icon in Toolbar or select Window Menu->Scenes) and add a Scene (click Add button on Scene Dialog). In the Create New Scene Dialog, edit the name and description for the new scene and then press the OK button. Note that by default, new annotations are added to the current scene and stored in the scene file. If one wants to place annotations into a disk file, click the small arrow to the right of the Scene button in the Insert New section of the Toolbar. When the arrow is clicked, a menu is displayed for creating and/or selecting a disk annotation file.

9. Save the Scene File. Click Save As button the first time to set the path and name of the scene file. Once path and name of scene file has been set, use the Save button.To set the name of the New Scene File, click the Save As button. In the file selection dialog, choose the directory, and enter a descriptive name for the Scene File. It is best for the Scene File to be in the same directory or the parent directory of the directory containing your data files. If the data files are scattered about many directories, it may cause problems if the Scene File and its data files are zipped for distribution to others or when uploading the BALSA Database

10. Repeat last few steps to edit annotations and create additional scenes.

11. If the Save button at the top of the Scene Dialog is enabled, the Scene File is in a modified state. Click the Save button to save the Scene File and avoid losing your work.

Understanding the Tab and Window Coordinate Spaces

In PowerPoint, each slide maintains a fixed aspect ratio (the ratio of height to width remains constant) with a spatial coordinate system (typically inches). As a result, each annotation in PowerPoint is places its annotions at a spatial coordinate (X and Y in inches). In contrast, wb_view defaults to a variable aspect ratio so that the window is resizable to best fit the brain model (surface, volume, chart). This variable aspect ratio is problematic for annotations in Tab or Window Space both of which use a percentage coordinate system (0% at left/bottom and 100% at right/top).

If one creates a Tab Space annotation with the variable aspect enabled and changes the size of the window, the Tab Space annotation may no longer be in the correct location. To correct this problem, wb_view supports “locking of the aspect ratio”. When the aspect ratio is locked, the window (and each tab within the window) are fixed to the aspect ratio at the time aspect locking is enabled. If the size of the window changes while the aspect is locked, the contents of window and each tab will expand or contract in size but maintain a fixed aspect by adding space to sides of the model when needed.

Scenes

Scenes are closely related to annotations. Scenes allow one to preserve 'the state’ of wb_view. Thus one if one saves a scene, exits wb_view, later restarts wb_view, and loads the scene, wb_view appears identical to when the scene was originally saved. Scenes are frequently used for figures in publications. Scenes are also uploaded to the BALSA database for sharing with other users.

While annotations can be saved in disk files, annotations are most commonly saved to a scene. When creating annotations for a scene, it is a best practice to save the annotations to the scene instead of creating a disk annotation file.