Appion

r17333 adds the feature in apDDprocess.py and activate the function in apK2process.py

This works only for counting mode. Linear mode images would be too noisy to predict the good threshold to give only debris shadow.

Assign to Kuanglei Tsai to test. He will probably the next person using K2 counted mode and need to align frames.

Kuang-Lei, just run the makeDDRawFrameStack.py script as usual with --align option when you collect your counted mode data. The committed aligned image should not show the "hair".

The code looks mostly good. There are two minor issues I notice.

On line 521 (executed if correctFrameImage is called with stripe_correction=True), getStripeNormArray is called with length=512.
Are we sure we want to hard-code the length there? I'm not sure but it could be a leftover from the coding process.

On line 547, I'm confused shape=array.shape because when I make a numpy array and access the shape attribute, I get a type error, "'tuple' object is not callable."

It looks like getStripeNormArray() casts the variable 'length' as an integer (line 534.)
If length is an integer, and shape a tuple, than I doubt that '>' overloads properly to allow for the conditional on line 548. There's a clue that I'm wrong about length being an integer, though, because of the casting on line 550.

Ryan,

Thanks for your great effort in an excellent code review and sorry for not getting back to you earlier.

I should have explained that when you view diff for a particular file linked in the revision, the red code block is the code that is deleted in the revision, and therefore, no longer exists in the code. I should also mentioned that I deleted getStripeNormArray function because it never worked right. To be correct, I should have committed two revisions.

Regarding array.shape, I suspect that you did

array.shape()

not

array.shape

when you got that error. Getting value of attributes does not require () in python.

As for the bad casting, you are absolutely right. It shows you how behind we are in code review. When we did use it, the image was always much larger, so the expected boolean False resulted even though they should not be used for comparison.

You can close this issue after you read this. Several people have used this feature so far, and we no longer have K2. Gatan promised that the new camera software with the new one won't need our effort for this matter.