CONFETTI/runAllfiber.script at main · styner/CONFETTI · GitHub

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#!/bin/tcsh

set nonomatch

set doAlways = 0

if (! -e ./FiberAxis) mkdir ./FiberAxis
if (! -e ./FiberAxisProfiles) mkdir ./FiberAxisProfiles
if (! -e ./OutputMerged) mkdir ./OutputMerged

foreach i (./Fibers/*parametrized.vtk)
	if (! -e ./FiberAxis/$i:t:r_axis.vtk || $doAlways == 1) then
		echo computing axis for fiber $i
		python ./compute_fiber_axis.py $i --legacy --outlier-sigma 4.0 --clip-factor 3.0 -o ./FiberAxis/$i:t:r_axis.vtk --profiles-dir ./Profiles/  --profiles-output-dir ./FiberAxisProfiles/
	endif
end
if (! -e ./OutputMerged/Fibers_merged.vtk || $doAlways == 1) then
echo merging fibers
	python ./merge_fibers.py ./Fibers -o ./OutputMerged/Fibers_merged.vtk
endif

if (! -e ./OutputMerged/FiberAxis_merged.vtk || $doAlways == 1) then
	echo merging fiber axes
	python ./merge_fibers.py ./FiberAxis -o ./OutputMerged/FiberAxis_merged.vtk
endif

if (! -e ./OutputMerged/FiberAxisProfiles_merged.vtk || $doAlways == 1) then
	echo merging fiber axis profiles
	python ./merge_fibers.py ./FiberAxisProfiles -o ./OutputMerged/FiberAxisProfiles_merged.vtk
endif

if (! -e ./OutputMerged/FiberAxisProfiles_merged_imputed.vtk || $doAlways == 1) then
	echo impute missing values with INR
	python impute_missing_profiles.py ./OutputMerged/FiberAxisProfiles_merged.vtk --epochs 200 --omega-0 10
endif

if (! -e ./OutputMerged/FiberAxisProfiles_merged_imputed_neighborhood_L5.vtk || $doAlways == 1) then
	echo build neighborhood graph
	python build_neighborhood_graph.py ./OutputMerged/FiberAxisProfiles_merged_imputed.vtk --levels 6
endif