separate wrapper function

[ngreenwald]

This provides a way for us to modify the post-processing params that are sent to the consumer.

Let me know if you think it would be better to have this somewhere else before I start moving forward

[willgraf]

I think the consumer itself is still using multiplex_postprocess instead of the new value.

[ngreenwald]

It's the only one that's different from the defaults in deepcell_toolbox. Should we move all of the defaults to here?

…

On Mon, Sep 21, 2020 at 12:22 PM willgraf ***@***.***> wrote: ***@***.**** requested changes on this pull request. I think the consumer itself is still using multiplex_postprocess instead of the new value. ------------------------------ In redis_consumer/processing.py <#131 (comment)> : > + if whole_cell_kwargs is None: + whole_cell_kwargs = {} + whole_cell_kwargs['radius'] = 5 + + if nuclear_kwargs is None: + nuclear_kwargs = {} + nuclear_kwargs['radius'] = 5 Is radius the only one we want to default? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#131 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJB47NPTWVYYQLSJFR4VYDSG6RVZANCNFSM4RSO57HA> .

[ngreenwald]

Actually nevermind, I'm going to update them with the newest post-processing values, so I'll update all of them, and set the defaults here. Will make things easier to update moving forward. On Mon, Sep 21, 2020 at 1:44 PM Noah Greenwald <noahfgreenwald@gmail.com> wrote:

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It's the only one that's different from the defaults in deepcell_toolbox. Should we move all of the defaults to here? On Mon, Sep 21, 2020 at 12:22 PM willgraf ***@***.***> wrote: > ***@***.**** requested changes on this pull request. > > I think the consumer itself is still using multiplex_postprocess instead > of the new value. > ------------------------------ > > In redis_consumer/processing.py > <#131 (comment)> > : > > > + if whole_cell_kwargs is None: > + whole_cell_kwargs = {} > + whole_cell_kwargs['radius'] = 5 > + > + if nuclear_kwargs is None: > + nuclear_kwargs = {} > + nuclear_kwargs['radius'] = 5 > > Is radius the only one we want to default? > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#131 (review)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ADJB47NPTWVYYQLSJFR4VYDSG6RVZANCNFSM4RSO57HA> > . >

[willgraf]

Yeah I think it makes sense to add all the values here so they're easier to tweak moving forward.

[ngreenwald]

Okay, I updated it so there are defaults for all of them.

Currently, the consumer post-processing function doesn't take additional arguments. This doesn't matter right now, since there's no way for users to control any of the post-processing parameters. Eventually, we might want to add that option to the ImageJ app or deepcell.org. When then happens, we'd need to add a way for the base post-processing class to handle additional arguments.

However, since right now this doesn't exist, I set it up so that the 'defaults' are always used.

[willgraf]

This looks good, but I'd like to test the consumers out before we merge it.

[ngreenwald]

Yup, deepcell.org and ImageJ both gave good looking results