search

PreibischLab / BigStitcher

ImgLib2/BDV implementation of Stitching for large datasets
GNU General Public License v2.0
66 stars 14 forks source link

All Views fusion only uses selected images #40

Open mpinkert opened 5 years ago

mpinkert commented 5 years ago

I've found some behavior in the fusion code that may be a bug or just a misunderstanding on my part. Selecting a single (or group of) tiles in the Stitching Explorer and then doing an Advanced Fusion using the "All Views" bounding box outputs an image that covers the bounding box volume, but which only has values in the selected tile.

I understand this may be intentional to deal with different channels/illuminations/etc, as in Quick Fusion, but the behavior took me by surprise. If it is intentional, could we move the warning box in the Quick Fusion section of the documentation to the top of the Fusion page and make it clear that it applies to both types of fusion? It may be a good idea to add a warning to the Advanced Fusion GUI as well.

I've attached an image of the setup below. This fusion was done in the March 6th 0.3.1 snapshop of multiview-reconstruction and the 0.3.0 version of BigStitcher.

image

hoerldavid commented 5 years ago

Hi @mpinkert,

I think this is just a misunderstanding. The Bounding Box selection only defines the volume in which the fusion is done. What images are actually included is defined by what you have selected in the main window.

So in your case, selecting the "All views" bounding box, but just a single image will indeed produce an image that could fit all images but is blank save for the one image you selected.

The warning on the wiki page is about a slightly different issue: In the quick fusion, we will produce exactly one output image, fusing all selected images. E.g. if you select a multi-channel image, the quick fusion will just average the channels into one fused image. In the advanced fusion, you can group the images to be fused into multiple images with the Produce one fused image for: option to produce e.g. one fused image for each timepoint & channel (default).

I hope this explains the behaviour. It is as-intended from our part but I agree that it might be a bit confusing... Don't hesitate to ask if you have further questions :)

Best, David

mpinkert commented 5 years ago

Hi @hoerldavid,

Thanks for the thorough explanation. This does make sense now. I was pretty sure it was a misunderstanding, but I wanted to bring it up because if it tripped me up for a bit, it could do the same to others in the future, and it would be good to have this recorded for posterity.