Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

It isn't possible to run cell detection on channels with " in the name #1022

Closed
petebankhead opened this issue Jul 21, 2022 · 0 comments · Fixed by #1024
Closed

It isn't possible to run cell detection on channels with " in the name #1022

petebankhead opened this issue Jul 21, 2022 · 0 comments · Fixed by #1024
Labels
Milestone

Comments

@petebankhead
Copy link
Member

Bug report

Describe the bug
It isn't possible to run cell detection on channels with " in the name.

This has come up twice on the forum so far:

To Reproduce
Steps to reproduce the behavior:

  1. Open a fluorescence (non-RGB) image
  2. Change a channel name to "DAPI" or similar
  3. Try to run cell detection
  4. Observe an error - something pretty & informative like5.
Plugin error: com.google.gson.stream.MalformedJsonException: Unterminated object at line 1 column 23 path $.

Expected behavior
A " in a channel name isn't a good idea, but it shouldn't be a deal breaker.

Desktop (please complete the following information):

  • OS: All
  • QuPath v0.3.2 and earlier

Additional context
The root cause is my dodgy JSON-converting code at https://github.com/qupath/qupath/blob/main/qupath-core/src/main/java/qupath/lib/plugins/parameters/ParameterList.java#L585

Switching to use GsonTools should resolve it, but this will need a bit of care to ensure nothing breaks along the way.

@petebankhead petebankhead added this to the v0.4.0 milestone Jul 21, 2022
petebankhead added a commit to petebankhead/qupath that referenced this issue Jul 21, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant