3399fe3db90936ecc60d25307625afc7967ddbd4,programs/e2boxer.py,boxerTopaz,do_autobox_all,#,1382

Before Change

		pixradius  = int(diameter / (2 * downsample))
		boxsize    = boxerTopaz.boxerwindow.vbbsize.getValue()

		launch_childprocess(f". {boxerTopaz.conda_init_path} && {boxerTopaz.conda_activate_cmd} && topaz extract topaz/processed/micrographs/*.mrc --model topaz/model_epoch10.sav --radius {pixradius} --threshold {threshold} --num-workers {threads} --output topaz/processed/predicted_particles/predicted.txt ;echo")
		launch_childprocess(f". {boxerTopaz.conda_init_path} && {boxerTopaz.conda_activate_cmd} && topaz convert -x {downsample} -o topaz/processed/predicted_particles/all_predicted_full.txt topaz/processed/predicted_particles/predicted.txt ;echo")

		with open(f"topaz/processed/predicted_particles/all_predicted_full.txt", "r") as f:
			next(f)

After Change

		pixradius  = int(diameter / (2 * downsample))
		boxsize    = boxerTopaz.boxerwindow.vbbsize.getValue()

		boxerTopaz._launch_childprocess(f"topaz extract topaz/processed/micrographs/*.mrc --model topaz/model_epoch10.sav --radius {pixradius} --threshold {threshold} --num-workers {threads} --output topaz/processed/predicted_particles/predicted.txt ;echo")
		boxerTopaz._launch_childprocess(f"topaz convert -x {downsample} -o topaz/processed/predicted_particles/all_predicted_full.txt topaz/processed/predicted_particles/predicted.txt ;echo")

		with open(f"topaz/processed/predicted_particles/all_predicted_full.txt", "r") as f:
			next(f)
			newboxes = [("micrographs/"+(line.split()[0])+".hdf",int((line.split())[1]),int((line.split())[2]),"auto_topaz") for line in f]

Instances