Tile picker tool for fixed ROIs

[raacampbell]

Workflow:

1. User draws a fixed ROI.
2. User presses "tile-picker" which overlays tiles onto image.
3. Current tile under the mouse is highlighted.
4. Clicking will select/unselect each tile
5. User presses "DONE" and the tile pattern is then used to image the sample

[raacampbell]

Maybe do this with a ROI polygon? e.g.

>> imagesc(peaks(400))
>> R=drawpolygon(gca)

R = 

  Polygon with properties:

    Position: [14x2 double]
       Label: ''
       Color: [0 0.4470 0.7410]
      Parent: [1x1 Axes]
     Visible: 'on'
    Selected: 0

  Use GET to show all properties

The points, of course, are:

plot(R.Position(:,1),R.Position(:,2),'ok-')

And we can make them into a binary mask as follows:

p=R.Position;
M=poly2mask(p(:,1),p(:,2),400,400);
imagesc(M), axis xy

Then we can loop through all tile positions and look for overlap. If it exists, we keep the tile:

>> p=[150,90,50,50]; % Tile position [x,y,width,height]
>> x=[150,200,200,150]; 
>> y=[90,90,140,140];
>> T=poly2mask(x,y,400,400);             
>> imagesc(T)
>> imagesc(T+M)

[raacampbell]

The above solves the problem of how to select the tiles, but we also need to ensure we can build a non-rectangular tile pattern and have BakingTray image that. To test this, I set up a dummy session and take a preview. We can no visualise the current tile pattern with:

 hBTview.view_acquire.overlayTileGridOnImage(hBT.currentTilePattern)

and remove that with:

hBTview.view_acquire.removeOverlays('tilegrid')

Re-running overlayTileGridOnImage will replace the already plotted pattern. Not overlay another on top of it.

I can remove the first and last tiles and re-plot:

hBT.currentTilePattern(1,:)=[];
hBT.currentTilePattern(end,:)=[];
hBTview.view_acquire.overlayTileGridOnImage(hBT.currentTilePattern)

Indeed the tiles disappear. So that is an easy way of doing the tile-picking, TBH. Problems that will stop this:

1. BT.bake runs BT.populateCurrentTilePattern on line 127 if the user has selected "tiled: manual ROI". This wipes the modified grid.
2. If we comment out the above, it fails to cut and aborts because the number of tiles is not what was expected: BT.tilesRemaining returns false. Worse still, this is because length(hBT.positionArray) does not equal length(hBT.currentTilePattern)

Let's therefore first work on fixing point 2, to avoid this mis-match happening. Then we can figure out how best to by-pass point 1.

[raacampbell]

I have modified BT.populateCurrentTilePattern to handle non-rectangular tile scenarios. It does this by removing from a rectangular grid specified tiles or only keeping specified tiles from the grid. (6985844)

Now the question is how to allow the user to easily define this. In other words, somehow bake needs to know what the user intends to do regarding the tile pattern. Presumably this has to be part of the recipe or it does not make sense.

[raacampbell]

I now have added recipe.mosaic.tilesToRemove (e254580). This is expected to be a vector of tiels to remove from the final array. No error-checking yet but it's honoured when the tile grid is made, which makes it easy to work with. So the previous commit that works in BT.populateCurrentTilePattern is not needed. We leave it there regardless but note that the feature is dormant for now.

[raacampbell]

Add a basic tile picker GUI (ebd6180) that is based on a tile removal vector in the recipe mosaic structure (e254580, 84deda9). This is dev branch. For instructions see:

 help BakingTray.gui.acquisition_view.spawnTilePickerWindow