process_neighbourhoods

#!/bin/bash

new_sphere_r=0.34
length_reject_threshold=0.005
inclusion_radius=0.13 
perturb=0.0075
degree=3
ref_image_degree=20
neigh_size=3
vox_size=0.15

new_sphere_d=0.78
inclusion_diameter=0.26 


neigh_pattern=${1##*/}
base_path=${1%/$neigh_pattern}
output_path=$2

for neigh_path in `ls $1*`; do 

  neigh_file=${neigh_path##*/}

  neigh=${neigh_file:$(( ${#neigh_pattern} + 1 )):$(( ${#neigh_file} - 5 - ${#neigh_pattern} ))}
  echo $neigh

  

#  rm -r $base_path/$neigh

#  mkdir $base_path/$neigh
#  mkdir $base_path/$neigh/images
#  mkdir $base_path/$neigh/metropolis_hastings
#  mkdir $base_path/$neigh/strands


#  mkdir $base_path/$neigh/metropolis_hastings/A


#  cp $base_path/$neigh_file $base_path/$neigh/strands/cube.tck


#  trim_tcks $base_path/$neigh/strands/cube.tck $base_path/$neigh/strands/ball.tck -new_sphere_r ${new_sphere_r} -length_reject_threshold ${length_reject_threshold}

#  peel_tcks $base_path/$neigh/strands/ball.tck $base_path/$neigh/strands/peeled.tck -inclusion_radius $inclusion_radius

#  tck2fourier $base_path/$neigh/strands/peeled.tck $base_path/$neigh/strands/peeled.frr -degree ${degree}
 
#  perturb_fouriers $base_path/$neigh/strands/peeled.frr $base_path/$neigh/metropolis_hastings/A/initial.frr -perturb $perturb

#  rm  $base_path/$neigh/images/tophat.mif 

#  tck2fourier $base_path/$neigh/strands/$neigh_pattern.tck $base_path/$neigh/strands/cube_for_ref.frr -degree $ref_image_degree

#  expected_image $base_path/$neigh/strands/cube_for_ref.frr /data/home/tclose/Data/Gradient_directions/encoding_60.b $base_path/$neigh/images/tophat.mif -vox_size ${vox_size} -num_voxels 3 -points 100

# tck2fourier  $base_path/$neigh/strands/sphere_0.78.tck  $base_path/$neigh/strands/ball.frr -degree 3

# cp $base_path/$neigh/strands/ball.frr $output_path/ball_combined/$neigh.frr

#echo $neigh_count

#mv $base_path/$neigh/strands/cube_1.05.tck $base_path/$neigh/strands/cube.tck

#mv $base_path/$neigh/strands/sphere_0.78.tck $base_path/$neigh/strands/ball.tck

#rm $base_path/$neigh/strands/cube_1.05-frr_20.frr

#rm $base_path/$neigh/strands/sphere_0.78*

#tcks2fouriers $base_path/$neigh/strands/ball.tck $base_path/$neigh/strands/ball.frr -degree 3
  
ln -s $base_path/$neigh/strands /data/home/tclose/Data/Tractography/chunked/vox_0.15/strands/$neigh_count

#ls $base_path/$neigh/strands

#neigh_count=$(( $neigh_count + 1 ))

done