skeletonH5XfmSpeedup

#!/bin/bash
# Measure time for transforming skeletons withs nii dfields vs h5 dfields

## SMALL H5
smallStart=$(date +%s%N)
transformSwc -s GadMARCM-F000122_seg001_03.swc \
    -o GadMARCM-F000122_seg001_03_toJRC2018small.swc \
    -t JRC2018F_FCWB_small.h5??i
smallEnd=$(date +%s%N)
echo "smallStart,$smallStart"
echo "smallEnd,$smallEnd"
smallTime=$(echo "($smallEnd - $smallStart)/1000000" | bc)
echo "smallTime,$smallTime"


## Big H5
bigStart=$(date +%s%N)
bigH5="/groups/saalfeld/public/jrc2018/transformations/quantized_multiscale/JRC2018F_FCWB.h5"
transformSwc -s GadMARCM-F000122_seg001_03.swc \
    -o GadMARCM-F000122_seg001_03_toJRC2018.swc \
    -t ${bigH5}??i
bigEnd=$(date +%s%N)
echo "bigStart,$bigStart"
echo "bigEnd,$bigEnd"
bigTime=$(echo "($bigEnd - $bigStart)/1000000" | bc)
echo "bigTime,$bigTime"

# Raw ants outputs
affine="/groups/saalfeld/public/jrc2018/transformations/jrc2018F-FCWB/JRC2018F_FCWB_0Affine.mat"
fdfield="/groups/saalfeld/public/jrc2018/transformations/jrc2018F-FCWB/JRC2018F_FCWB_1Warp.nii"
idfield="/groups/saalfeld/public/jrc2018/transformations/jrc2018F-FCWB/JRC2018F_FCWB_1InverseWarp.nii"

antsStart=$(date +%s%N)
transformSwc -s GadMARCM-F000122_seg001_03.swc \
    -o GadMARCM-F000122_seg001_03_toJRC2018AntsInv.swc \
    -t ${affine}?i \
    -t ${idfield}
antsEnd=$(date +%s%N)

echo "antsStart,$antsStart"
echo "antsEnd,$antsEnd"
antsTime=$(echo "($antsEnd - $antsStart)/1000000" | bc)
echo "antsTime,$antsTime"


#############################################################
# This script produced the following output on 2019 Sept 26 #
#############################################################
#smallStart,1569523492033478557
#smallEnd,1569523494058777305
#smallTime,2025
# 
#bigStart,1569523494063696252
#bigEnd,1569523495817527854
#bigTime,1753
#
#antsStart,1569523495822603388
#antsEnd,1569523563795869723
#antsTime,67973