Unable to use wfntp due to use of a library function that is no longer valid
What happened?
When starting a job with wfntp, the following error message is logged to the console:
ValueError: Values other than "rc" for the "coordinates" argument to skimage.measure.regionprops are no longer supported. You should update your code to use "rc" coordinates and stop using the "coordinates" argument, or use skimage version 0.15.x or earlier.
Expected behaviour
wfntp should be able to compute measure normally
Environment
fedora 36
Conda environment set up as described
Steps to reproduce
Set up the conda environment as described in this repo, clone it and attempt to lauch wfntp and load then start a job, the bug should happen when computing the measures for the first frame
Relevant log output
The error was:
Traceback (most recent call last):
File "/home/jcts/Documents/goinfre/Elegant-Elegans/WF_NTP/WF_NTP/WF_NTP_gui.py", line 305, in run_tracker
print_data, bends = _run_tracker(settings, queue)
File "/home/jcts/Documents/goinfre/Elegant-Elegans/WF_NTP/WF_NTP/WF_NTP_script.py", line 121, in run_tracker
print_data, locations = track_all_locations(video, settings, stdout_queue)
File "/home/jcts/Documents/goinfre/Elegant-Elegans/WF_NTP/WF_NTP/WF_NTP_script.py", line 221, in track_all_locations
print_data = process_frame(settings, Z, mean_brightness,
File "/home/jcts/Documents/goinfre/Elegant-Elegans/WF_NTP/WF_NTP/WF_NTP_script.py", line 287, in process_frame
props = measure.regionprops(labeled_removed, coordinates='xy')
File "/home/jcts/.conda/envs/v_wf_ntp/lib/python3.8/site-packages/skimage/measure/_regionprops.py", line 1279, in regionprops
raise ValueError(msg)
ValueError: Values other than "rc" for the "coordinates" argument to skimage.measure.regionprops are no longer supported. You should update your code to use "rc" coordinates and stop using the "coordinates" argument, or use skimage version 0.15.x or earlier.
Description
Unable to use wfntp due to use of a library function that is no longer valid
What happened?
When starting a job with wfntp, the following error message is logged to the console: ValueError: Values other than "rc" for the "coordinates" argument to skimage.measure.regionprops are no longer supported. You should update your code to use "rc" coordinates and stop using the "coordinates" argument, or use skimage version 0.15.x or earlier.
Expected behaviour
wfntp should be able to compute measure normally
Environment
fedora 36 Conda environment set up as described
Steps to reproduce
Set up the conda environment as described in this repo, clone it and attempt to lauch wfntp and load then start a job, the bug should happen when computing the measures for the first frame
Relevant log output
Proposed solution
use rc coordinates as indicated in the log output