Crop tool improvements

[acardona]

A number of issues to address:

• [ ] Coordinates are in pixels rather than nanometers
• [ ] Can't enter values manually when none have been programmatically added yet via drawing the box
• [ ] Can't understand X and Y: are they local to the field of view? Is this an error?
• [ ] Can't scroll through sections
• [ ] Can't resize existing box without redrawing it
• [ ] Lack of persistence of values and box when selecting another tool
• [ ] Tick mark to trigger the crop is difficult to notice

[tomka]

@arcardona, I just factored the cropping tool's crop request generation into a separate CATMAID.crop() function. This should allow you to create the sub-volumes you wanted based on project space coordinates. Cropping a bouding box from (10, 11, 12) to (21,22,23) in the current project and active stack viewer's primary stack at zoom level 1 would look like this:

var stackId = project.focusedStackViewer.primaryStack.id;
CATMAID.crop(project.id, [stackId], 10, 11, 12, 21, 22, 23, 1);

You can optionally add a (clockwise) rotation around project Z as an extra parameter. The function returns a promise. So to do add a continuation to this call, use .then, e.g. CATMAID.crop(...).then(function() { console.log('done'); });.