Dynamic intensity scaling for CollectionViewer

[Thomas Caswell]

I strongly suggest finding a solution that does not involve changing
tifffile.py.  Managing those sort of changes will very quickly become
unsustainable.

Tom

On Tue, Mar 24, 2015 at 5:17 AM Ferdinand Greiss <ferdinand.greiss at gmail.com>
wrote:

>
> from skimage.viewer import CollectionViewer
>
> from skimage.viewer.plugins.lineprofile import LineProfile
>
> import numpy as np
>
> stack = np.random.randn(100, 50, 50)
>
> stack *= np.exp(-0.1*np.arange(stack.shape[0]))[:, np.newaxis, np.newaxis]
>
>
> viewer = CollectionViewer(stack)
>
> viewer += LineProfile()
>
> viewer.show()
>
>
> I actually did change the source code of tifffile.py written by Christoph
> Gohlke on line 4660 to include rescaling for min and max of current image
> in image stack (by pressing r). But it'd be nice to still be able to use
> your plugins...
>
>
> Thanks for your prompt answer...
>
> Ferdinand
>
> Am Montag, 23. März 2015 23:57:11 UTC+1 schrieb stefanv:
>>
>> Hi Ferdinand
>>
>> On Mon, Mar 23, 2015 at 8:15 AM, Ferdinand Greiss
>>
> <ferdinan... at gmail.com> wrote:
>> > I was wondering whether it would be straight forward to implement
>> automatic
>> > rescaling of intensity (or y axis on LineProfile widget) in order to
>> account
>> > for bleaching in image sequences. Otherwise the line plot will vanish
>> below
>> > the pre-computed value of the first image and I won't be able to see
>> much
>> > after the first few images.
>>
>> I think that should be pretty simple.  Can you share a code snippet of
>> how you are using it currently?
>>
>> Stéfan
>>
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