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@bnmajor bnmajor commented May 20, 2025

This PR provides a solution for projects that may not have a previous job id associated with them (which was required in order to request further training). As an alternative, the values typically set in the initial superpixel generation step can be set in the .histomicsui_config.yaml file:

  • radius: The size of superpixels generated (UI defaults to 100)
  • magnification: The magnification level at which to generate the superpixels (UI defaults to 5)
  • certainty: The metric used to determine the order that predictions are presented to the user (UI defaults to confidence). Options are confidence, margin, negative_entropy, or batchbald.
  • feature: The feature shape. Either superpixel image data (image) or foundation model vector (vector). The UI defaults to image.

If training is requested and there is no job id and the radius, magnification, certainty, and/or feature keys are not set in the config file, you will be notified of which are missing and have the option to open the config and set the missing values.

image

NOTE: There is a bug around setting values in the config. Specifically, if a string value is set with single quotes (for example feature: 'image') at the end of the file and there is a new line at the end (either added manually or automatically by using the Format button) then the UI is not automatically notified of the change and will think that the value is still missing. This can be avoided by any of the following:

  • not listing string values last
radius: 100                        certainty: 'confidence' 
magnification: 5                   feature: 'image'
certainty: 'confidence'     ->     radius: 100
feature: 'image'                   magnification: 5
  • not using quotes around the string value
feature: 'image'     ->     feature: image
  • refreshing the UI after updating the config file

@bnmajor bnmajor changed the title No job No job ID May 20, 2025
@bnmajor bnmajor marked this pull request as draft May 20, 2025 13:38
@bnmajor bnmajor marked this pull request as ready for review May 27, 2025 14:48
@bnmajor bnmajor requested a review from manthey May 27, 2025 14:49
@manthey
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manthey commented May 28, 2025

When I start a new project the normal way I've been doing it, I get a job failure: SuperpixelClassification.py: error: argument --magnification: invalid parseValue value: ''

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bnmajor commented Jun 19, 2025

When I start a new project the normal way I've been doing it, I get a job failure: SuperpixelClassification.py: error: argument --magnification: invalid parseValue value: ''

This has been resolved

@bnmajor bnmajor marked this pull request as draft June 19, 2025 14:31
@bnmajor bnmajor marked this pull request as ready for review June 19, 2025 16:45
@bnmajor bnmajor merged commit b098c0f into master Jun 19, 2025
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@bnmajor bnmajor deleted the no-job-id branch June 19, 2025 17:39
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3 participants