duke-lungmap-team / lungmap-pipeline Goto Github PK

I'm adding instructions to the README to tell users how to get their own copy of the data for running the example pipelines. However, currently the lungmap-image-data repository only contains 20x images. How will we handle the 60X examples?

@whitews - In order to generate evaluations, I need to stash a few utility functions. Considering creating an examples/utils folder for this purpose. Please verify this is acceptable?

Using ontospy==1.9.8.2, I'm getting a fatal error in gui.utils when trying to instantiate an ontospy.Ontospy object. The error is:

Fatal error parsing graph <../resources/lung_ontology.owl>
(using RDF serializations: ['xml'])

On Windows 10, upon selecting default settings and then selecting the image *_001.tif and then pressing Find Regions, the pipeline starts to find contours and we see the following in the console:

Pre-processing test image...
90 color candidates found, kernel: (15, 15)

at which point a new blank LungMAP Region Generator Image screen populates. This is occurring in lungmap_pipeline.Application.run_segmentation. Not sure if threading from find_regions is the culprit. Let me know if you have ideas about tracking this down.

In debugging, it looks like this is failing in cv2_extras.utils.find_border_by_mask, specifically, for some contours the function scipy.optimize.curve_fit is being fed a range, which doesn't have a shape attribute. Let me know if you can replicate.