added files

algorithm_outline.txt

@@ -0,0 +1,32 @@
+MR::Math::Matrix(points, point_conv, strand.matrix()) 
+MR::Math::Matrix(tang, tang_conv, strand.matrix()) 
+
+(VoxelSize, ResponseFunction, parameters to Image class)
+
+BTS::Image<Interpolator>::Neighbourhood::reserve() --set initially to some reasonable number
+BTS::Image<Interpolator>::Neighbourhood::add_section(points.row(x), tang.row(x), *strand, point_conv.row(x), tang_conv.row(x)) (maybe include pointers to intermediately generated structures as well)
+
+BTS::Image<Interpolator>::Neighbourhood::calculate_intensities()
+	internally store points in a Nx3 matrix and tangents in a Nx3 matrices
+	have the list of voxel centres as Lx3 matrix and dw orientations as a 3xQ matrix  
+	Then should have a LxNx3 distance array, Nx1 length vector, and a NxQ angle matrix.  
+
+	response_functions as a NxQ matrix (will need to to column-wise multiplication and collecting on angle matrix) to produce another NxQ response matrix. 
+
+	columnwise multiplication of length_vector and angle matrix produces another NxQ matrix (probably could be incorporated into response function step I think)
+
+	interpolation function operates on LxNx3 to produce LxN interpolation intensities
+
+	matrix multiplication produces LxQ intensity matrix.
+
+BTS::Image<Interpolator>::collate_neighbourhoods(Neighbourhood)
+
+	takes LxQ matrices from neighbourhoods and collates them into L'xQ image data matrix.
+
+BTS::Image<Interpolator>::Neighbourood::calculate_gradients_hessians
+	Then take collated intensities and put them back into the calculate the gradient + Hessian
+	 reusing the precalculated interpolation and response matrices.
+
+
+	BTS::Image<Interpolator>::collate_gradients_hessians(Neighbourhood)
+		this is done per neighbourhood calculation to prevent large memory allocation problems

bash/add_base_intensity

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+DIR=$1
+
+if [ "${#DIR}" = 0 ]; then
+  DIR='.'
+fi
+
+for f in `ls $DIR/*.tck`; do 
+
+  if [ -h $f ]; then
+    file=`readlink $f`
+  else
+    file=$f
+  fi
+
+  file_strip=${file##*/}
+
+  select_fibres $file /tmp/$file_strip.txt
+
+  sed -i 's/base_intensity: 0/base_intensity: 1/g' /tmp/$file_strip.txt
+
+  select_fibres /tmp/$file_strip.txt $file
+
+done

bash/add_density

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+DIR=$1
+
+if [ "${#DIR}" = 0 ]; then
+  DIR='.'
+fi
+
+for f in `ls $DIR/*.tckx`; do 
+
+  if [ -h $f ]; then
+    file=`readlink $f`
+  else
+    file=$f
+  fi
+
+  if [ `grep -c "density" $file` = 0 ]; then
+
+    sed -i 's/^/1\t/g' $file
+
+    sed -i 's/1\t%%% Extended Properties File %%% - keys: /%%% Extended Properties File %%% - keys: density\t/g' $file
+
+  fi
+
+done

bash/create_fibres

@@ -0,0 +1,30 @@
+#!/bin/bash
+
+#if [ $# -le 1 ]; then
+#  echo "At least 1 argument need to be supplied to $0 ($# supplied)."
+#  exit -1
+#fi
+
+if [ ${1##*.} == 'txt' ]; then
+
+  new_fibres $1 ${@:2}
+
+  vi $1
+
+else
+
+  TEMP_TXT_FILE=/tmp/${1##*/}.txt
+
+  #Export fibres file to a temporary text equivalent.
+  new_fibres $TEMP_TXT_FILE ${@:2} 
+
+  #Edit with vi
+  vi $TEMP_TXT_FILE 
+
+  #Import fibres back to output location
+  select_fibres $TEMP_TXT_FILE $1
+
+  #Cleanup temporary file
+  rm $TEMP_TXT_FILE
+
+fi

bash/edit_fibres

@@ -0,0 +1,28 @@
+#!/bin/bash 
+
+if [ $# == 0 ]; then
+  echo "No arguments supplied to $0 (at least 1 required)."
+  exit -1
+elif [ $# == 1 ]; then
+  OUTPUT_LOCATION=$1
+elif [ $# == 2 ]; then
+  OUTPUT_LOCATION=$2
+else
+  echo "Too many arguments ($#) supplied to $0 (max 2, input and output locations)."
+  exit -1
+fi
+
+
+TEMP_TXT_FILE=/tmp/${1##*/}.txt
+
+#Export fibres file to a temporary text equivalent.
+select_fibres $1 $TEMP_TXT_FILE
+
+#Edit with vi
+vi $TEMP_TXT_FILE 
+
+#Import fibres back to output location
+select_fibres $TEMP_TXT_FILE $OUTPUT_LOCATION
+
+#Cleanup temporary file
+rm $TEMP_TXT_FILE

bash/metropolis

@@ -0,0 +1 @@
+../metropolis_release/tractography

bash/process_collections

@@ -0,0 +1,43 @@
+#!/bin/bash
+
+export neigh_count=0
+
+neigh_size=3
+vox_size=0.15
+extent=3
+neigh_bounds=0.61
+cube_size=1.05
+
+input_dir=/data/home/tclose/Data/Fifty_phantoms/
+output_dir=/data/home/tclose/Data/Tractography/chunked
+
+for collection_path in `ls $input_dir`; do
+
+  extension=${collection_path##*.}
+
+  if [ $extension = "tck" ]; then
+    coll_name=${collection_path##*/}
+    coll_name=${coll_name%.*}
+
+    echo "--$coll_name--"
+
+#    rm -r $output_dir/${coll_name}/vox_${vox_size}
+#    mkdir $output_dir/${coll_name}/vox_${vox_size}
+
+#    chunk_strands $input_dir/$collection_path $output_dir/${coll_name}/vox_${vox_size}/cube_${cube_size}.tck -extent $extent -voxel_size $vox_size -map_to_origin -save_separate -half_offset -neigh_bounds $neigh_bounds
+
+#    rm -r $output_dir/${coll_name}/vox_${vox_size}/ball_combined
+#    mkdir $output_dir/${coll_name}/vox_${vox_size}/ball_combined
+
+    process_neighbourhoods $output_dir/${coll_name}/vox_${vox_size}/cube_${cube_size} $output_dir/${coll_name}/vox_${vox_size}
+
+#   ls $output_dir/${coll_name}/vox_${vox_size}/prepared_strands $output_dir/prepared_strands/${coll_name}.frr
+
+    #combine_strands $output_dir/${coll_name}/vox_${vox_size}/ball_combined $output_dir/ball_combined/${coll_name}.frr
+
+  fi
+
+done
+
+
+#combine_strands $output_dir/ball_combined/ $output_dir/ball_combined.frr

bash/process_neighbourhoods

@@ -0,0 +1,79 @@
+#!/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

bash/rename_frr

@@ -0,0 +1,24 @@
+#!/bin/bash
+
+directory_name=$1
+
+for file in `ls $directory_name/*.frr`; do 
+
+   svn move $file ${file/%.frr/.str}; 
+
+done
+
+for file in `ls $directory_name/*.frrx`; do 
+
+   svn move $file ${file/%.frrx/.strx}; 
+
+done
+
+for file in `ls $directory_name/*.frrxx`; do 
+
+   svn move $file ${file/%.frrxx/.strxx}; 
+
+done
+
+
+svn commit -m "renaming '.frr' to '.str' in directory $directory_name"

bash/test_bed

@@ -0,0 +1 @@
+../test_bed/tractography

build

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+#TARGET='src/bts/fibre/base.o'
+#TARGET='bin/stress_tester'
+
+if [ ${#TARGET} -gt 0 ]; then
+
+  echo
+  echo "WARNING!! Only building for target $TARGET"
+  echo
+
+
+fi
+
+/home/tclose/Code/MRtrix/build $TARGET $@
+

build_debug

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+#CMD_TARGET='dummy'
+#OBJ_TARGET='fibre/tractlet/set/walker'
+
+if [ ${#CMD_TARGET} -gt 0 ]; then
+
+  echo
+  echo "WARNING!! Only building for target $CMD_TARGET"
+  echo
+
+  TARGET=bin/${CMD_TARGET}__debug
+
+elif [ ${#OBJ_TARGET} -gt 0 ]; then
+
+  echo
+  echo "WARNING!! Only building for target $OBJ_TARGET"
+  echo
+
+  TARGET=src/bts/${OBJ_TARGET}__debug.o
+
+fi
+
+echo $TARGET  
+
+/home/tclose/Code/MRtrix/build debug $TARGET $@