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Neural-Systems-at-UIO / nutil

https://nutil.readthedocs.io/en/latest/
GNU General Public License v3.0
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custom mask color in the nut file #235

Closed Majpuc closed 3 years ago

Majpuc commented 3 years ago

Hi, Even when the feature custom mask is not selected, the custom_mask_color = 255,255,255,255 is displayed in the nut file. Does it mean that this mask color is selected by default or should this line not be present in the nut file when custom mask=no is chosen?

sharoncy commented 3 years ago

As far as I'm aware the "custom_mask_color" field is not used by the Nutil code unless the mask feature is switched on. It also doesn't appear in the GUI unless the mask feature is switched on. And you're right. white (255,255,255,255) is the default mask colour here, so that is what appears if the user switches on the mask feature.

Majpuc commented 3 years ago

That is fine. Would it make sense that this line "custom color mask" is not listed in the nut file if the users select custom mask=no ? At first I though the users had activated this mask feature by looking at the nut file, then I realized that "no" was selected.

sharoncy commented 3 years ago

The NUT file always includes all the fields, so it is not an option to leave it out of the NUT file. It may be possible to have "blank" (no colour selected) as the default but I would have to ask @leuat about that. Is there a reason you're asking? Has a user been confused by this? We could add a more thorough description to the NUT part of the readthedoc if interpreting the NUT file is a problem. I think this is a good idea either way. https://nutil.readthedocs.io/en/latest/QuantifierOutput.html#nut-file

Majpuc commented 3 years ago

Great, now I know. I was the one confused during the troubleshooting. It is a good idea to add in the readthedocs. I am planning an FAQ paragraph for all the online docs. I can start a google doc on this that we could populate with questions that have arisen from users.

sharoncy commented 3 years ago

Sounds good. I already have FAQ for the ilastik part of the readthedoc. We could follow a similar structure for the other software: https://nutil.readthedocs.io/en/latest/Ilastik.html#faq-and-troubleshooting

Majpuc commented 3 years ago

Exactly! Very nice. I will close the issue now.