Slicer:Simbios Editing Modifications

This work is being done by Chand John at Stanford, working in Scott Delp's lab.

New Features Needed

Here are some features that people need for their own use (My Goals for the week):

1. Output original user points in millimeters, not pixels
2. Do proper coordinate system transformations for slice directions other than axial during Apply
3. ModelMaker should construct *closed* models: close up open areas with faces with normal vectors pointing outward
4. Semi-automatic segmentation of knee data: what is the best starting point?
5. Allow segmentation with contours in all directions, not just in-plane: output a point cloud and have marching cube construct a mesh from it still
6. Allow skipping slices during segmentation
7. Not just image-to-image registration, but also image-to-model and model-to-model registration
8. Display a polygon and its spline on the 3D model as you modify the polygon
9. Load a model from some other program and automatically reconstruct some control points for each slice so user can edit it in Slicer; basically intersect plane with model and sample some points; some programs will just give us these points (this is for users who constructed models in other programs and want to modify them in Slicer)
10. Make EdDraw's polygons/splines have subpixel accuracy: many users don't like the choppy pixel-level detail the polygons and curves have
11. People want a simple interface!! Not too many buttons they won't use, etc.
12. How to package Slicer so users don't have to build it themselves?
13. How to package Slicer into a WiseInstall or InstallShield program?

Already Updated in Slicer 2.4

Here is a list of features I have *already* added to Slicer 2.4 for use at Stanford:

1. Allowing inserting points between two existing points in a control polygon in the EdDraw module.
2. Automatic switching between Select and Move modes based on mouse location. Holding control key overrides this and allows selection of multiple groups of points. This makes editing a polygon much easier.
3. Fixed a bug for overcounting selected points--Steve said he checked this in already.
4. Can no longer plot multiple points by dragging the mouse while a button is pressed--this sometimes leads to too many points being plotted unnecessarily in one location. This change can be easily reversed if needed though.
5. A green cardinal (cubic C^1-continuous) spline is interpolated interactively though the control points of an active polygon in EdDraw.
6. A "Density:" textfield in EdDraw allows user to enter how many points to sample from each cardinal spline segment, in addition to the user-plotted control points, when Apply is clicked. Setting density to zero retains the original Slicer functionality, since it samples no additional points. Default is 3.
7. I added a data structure to hold all of the user-defined polygons drawn on every slice of data. It has a bug right now but it will allow storing multiple contours per slice. This data is needed for portability between other software used in our lab. It will be extended (see below).
8. An "Unapply" button in EdDraw, to allow modification of *any* polygon the user has drawn on *any* slice at *any* time. Frequently people make coarse segmentations on multiple slices and then refine them later.
9. CTRL+A shortcut for select all.
10. Cut (CTRL+X), Copy (CTRL+C), and Paste (CTRL+V) for polygons drawn in EdDraw.
11. Combined all edit operations into one menubutton.
12. Allow open and closed contours, both as points or as lines (extends Points, Polygons, Lines).
13. Added data structure from #7 to vtkMrmlDataVolume and added feature to output sampled user-defined polygons to a .pts output.
14. Added support for reading PGI amd MR files with names like <name>001.pgi.