A wbi align command

[vineetbansal]

The vb/qt branch has a script scripts/image_align.py that demonstrates a rough image alignment UI we can use going forward. Mostly thanks to https://github.com/marcel-goldschen-ohm/PyQtImageViewer

• Play with the gui and make sure you're comfortable with navigation/adding/deleting points. (Right click near a selected point to delete it). You can zoom in by drawing a box around an area and zoom out by right click. Pan using the middle mouse button and drag. Mouse scroll to move between frames.
• Pay attention to the data that goes in (the shape of it), the pre-populated points (if any), and the resulting points after the UI is closed.
• We will now integrate this gui as part of wbi.
• Assume the /bsa folder corresponds to the test alignment data folder we have from Junang.
• Currently the Experiment class cannot be instantiated unless we have a other-frameSynchronous.txt file, which we don't for the /bsa folder. This is a general problem with all these classes which I'll fix as a separate issue. For now comment out the lines:

        self.frames_sync = FrameSynchronous(folder_path)
        self.timing_dataframe = self.timing.merge_sync(self.frames_sync)

in the Experiment class constructor to proceed.

• e = Experiment('/bsa')
• e.median_images_himag() will give you M AxB images. For each of these img, img[:img.shape[0]/2, :] are the red channel images, img[img.shape[0]/2:,:] are the green channel images.
• e.median_images_lomag() will give you N CxD images.
• Take the smaller of M, N and start looking at each of the 2 himag and 1 lomag images in turn. You get min(M,N) x 3 total images.
• Bring up the gui as a result of a new wbi align command that you introduce (just the input folder is needed as an argument for now), where you see these 3 images, and can go from 0..min(M,N) time steps, and add points.
• Both the Qt* modules can be introduced inside a new wbi.ui module in our code.
  You can save the points as a text file for now.

Don't worry about polishing up the UI code - it's not worth the time right now, and we can do that as we go along. So you should not have to change anything in the Qt* modules at all.