Feature request: crop? about stackview HOT 10 CLOSED

It's fun cropping a dataset like this!

from stackview.

Hey @paxcalpt ,

great idea! Could you try out the very basic prototype in this notebook? I'm wondering if it works as expected.

If not, a PR on this notebook is very welcome!

also get those values?

You mean, like asking widget.get_start_x() or similar?

from stackview.

Beautiful!! Exactly what I needed.
As always, thank you for the lightening fast reply Robert

from stackview.

Hit a possible bug, will check if it might be on my side...

Running code:

from ipywidgets import IntSlider
import stackview

print(dataset.shape, dataset.dtype)

def crop(image, min_z:int, max_z:int, min_y:int, max_y:int, min_x:int, max_x:int):
    try:
        return image[min_z:max_z,min_y:max_y,min_x:max_x]
    except:
        return image

stackview.interact(crop,
                   dataset,
                   min_z=IntSlider(value=0, min=0, max=dataset.shape[0]-1),
                   max_z=IntSlider(value=dataset.shape[0]-1, min=0, max=dataset.shape[0]-1),
                   min_y=IntSlider(value=0, min=0, max=dataset.shape[1]-1),
                   max_y=IntSlider(value=dataset.shape[1]-1, min=0, max=dataset.shape[1]-1),
                   min_x=IntSlider(value=0, min=0, max=dataset.shape[2]),
                   max_x=IntSlider(value=dataset.shape[2]-1, min=0, max=dataset.shape[2]-1),
                  )

Output:

(500, 128, 128) uint16

TypeError Traceback (most recent call last)
File ~/Documents/Code/NanoPyx/.venv/lib/python3.10/site-packages/traitlets/traitlets.py:2395, in CInt.validate(self, obj, value)
2394 try:
-> 2395 value = int(value)
2396 except Exception:

TypeError: int() argument must be a string, a bytes-like object or a real number, not 'NoneType'

During handling of the above exception, another exception occurred:

TraitError Traceback (most recent call last)
Cell In[15], line 12
9 except:
10 return image
---> 12 stackview.interact(crop,
13 dataset,
14 min_z=IntSlider(value=0, min=0, max=dataset.shape[0]-1),
15 max_z=IntSlider(value=dataset.shape[0]-1, min=0, max=dataset.shape[0]-1),
16 min_y=IntSlider(value=0, min=0, max=dataset.shape[1]-1),
17 max_y=IntSlider(value=dataset.shape[1]-1, min=0, max=dataset.shape[1]-1),
18 min_x=IntSlider(value=0, min=0, max=dataset.shape[2]),
19 max_x=IntSlider(value=dataset.shape[2]-1, min=0, max=dataset.shape[2]-1),
20 )
23 # stackview.slice(dataset, continuous_update=True, zoom_factor=2, zoom_spline_order=0)
...
842 describe("the", value),
843 )
--> 844 raise TraitError(e)

TraitError: The 'step' trait of an IntText instance expected an int, not the NoneType None.

from stackview.

Confirmed to work =)... previous issue was solved by updating the package

from stackview.

Wait. We just played with the prototype ;-) This will now be refactored to be useful also for others ;-)

from stackview.

from stackview.

Alright, @paxcalpt, if you have some time for testing another prototype, please install

pip install stackview==0.5.1

It will come with a new crop function that looks like this:

I also updated the demo notebook. I would like to know from you if the capabilities for reading the range and/or cropping the image fulfills your use-case. Let me know if that works for you.

Btw. I was thinking of this crop widget earlier and wasn't sure how it should look like. Thus, thanks for the input! That was fun! 🌞

from stackview.

It's working perfectly! Bonus points for being VSCode rendering compatible

from stackview.

Awesome. Thanks again for triggering creative activities! 🥂

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