@wingillis just found that --bg-roi-depth-range should never equal to auto and the current setup may make the GUI tool unable to auto-detect parameters to generate config.yaml for ROI widget.
Since --bg-roi-depth-range is set to (650, 750) by default, and the type is expected to be (float, float), the flag should never equal a string. The current if statement shows that when autoset_depth_range is False, the depth will be auto-detected, but the auto-detection should happen when autoset_depth_range==True, which is more intuitive.
In the GUI, config.yaml is generated from default parameters from CLICK, therefore, the config.yaml needs to specify that the depth to be auto-detected.
Suggested changes:
moseq2_extract/cli.py line 61
function = click.option('--autoset-depth-range', is_flag=True, -> function = click.option('--autoset-depth-range', is_flag=True, default=True
When using the GUI function, the flag is set up in such a way that the depth can be automatically detected. When using the CLI, when there is a user input for --bg-roi-depth-range, the --autoset-depth-range is set to False and the user input range is used.
Updated suggested changes:
Instead of click.option('--autoset-depth-range', is_flag=True, maybe it's a better idea to click.option('--manualset-depth-range', is_flag=True,, the flag will default to False to trigger the automatic depth detection for GUI. Then when users specify '--manualset-depth-range', the bg-roi-depth-range will be set to user input value, and this option should have no default value.
aymanzay
commented
3 years ago
@wingillis just found that
--bg-roi-depth-rangeshould never equal toautoand the current setup may make the GUI tool unable to auto-detect parameters to generateconfig.yamlfor ROI widget.Since
--bg-roi-depth-rangeis set to(650, 750)by default, and the type is expected to be(float, float), the flag should never equal a string. The current if statement shows that whenautoset_depth_rangeisFalse, the depth will be auto-detected, but the auto-detection should happen whenautoset_depth_range==True, which is more intuitive.In the GUI,
config.yamlis generated from default parameters from CLICK, therefore, theconfig.yamlneeds to specify that the depth to be auto-detected.Suggested changes:
moseq2_extract/cli.pyline 61function = click.option('--autoset-depth-range', is_flag=True,->function = click.option('--autoset-depth-range', is_flag=True, default=True--bg-roi-depth-range, the--autoset-depth-rangeis set toFalseand the user input range is used.Updated suggested changes: Instead of
click.option('--autoset-depth-range', is_flag=True,maybe it's a better idea toclick.option('--manualset-depth-range', is_flag=True,, the flag will default toFalseto trigger the automatic depth detection for GUI. Then when users specify '--manualset-depth-range', thebg-roi-depth-rangewill be set to user input value, and this option should have no default value.