first, complete multi-shell-harmonization test

Author: tashrifbillah

lib/tests/pipeline_test.sh

@@ -0,0 +1,161 @@
+#!/usr/bin/env bash
+
+# ===============================================================================
+# dMRIharmonization (2018) pipeline is written by-
+#
+# TASHRIF BILLAH
+# Brigham and Women's Hospital/Harvard Medical School
+# tbillah@bwh.harvard.edu, tashrifbillah@gmail.com
+#
+# ===============================================================================
+# See details at https://github.com/pnlbwh/dMRIharmonization
+# Submit issues at https://github.com/pnlbwh/dMRIharmonization/issues
+# View LICENSE at https://github.com/pnlbwh/dMRIharmonization/blob/master/LICENSE
+# ===============================================================================
+
+
+EXIT()
+{
+    echo ''
+    echo $1
+    exit 1
+}    
+
+
+write_list()
+{
+    CASELIST=$1
+    TMPFILE=/tmp/harm_caselist.txt
+    while IFS=, read -r img mask; do echo $CURRDIR/$img,$CURRDIR/$mask; done < $1 > $TMPFILE
+
+    mv $TMPFILE $CASELIST
+}
+
+# get version info
+IFS=" = ", read -r _ v < ../../_version.py
+__version__=`echo $v | xargs`
+
+# download test data
+test_data=connectom_prisma # change this value if test data name is changed
+if [ ! -f ${test_data}.zip ]
+then
+    # we have been providing the same test data for the last couple of releases
+    # so no need to spend time uploading test data with each release for the forseeable future
+    # rather download from v2.0
+    __version__=2.0
+    wget https://github.com/pnlbwh/dMRIharmonization/releases/download/v${__version__}/${test_data}.zip
+fi
+
+tar -xzvf ${test_data}.zip
+
+cd ${test_data}
+CURRDIR=`pwd`
+
+# append path to image list and write back
+write_list connectom.txt
+write_list prisma.txt
+
+### Run pipeline and obtain statistics when same number of matched reference and target images are used in
+### tempalate creation and harmonization
+# run test
+../../multi-shell-harmonization.py \
+--template ./template-multi/ \
+--ref_list connectom.txt \
+--tar_list prisma.txt \
+--ref_name CONNECTOM \
+--tar_name PRISMA \
+--nproc -1 \
+--create --process --debug || EXIT 'multi-shell-harmonization.py with --create --process --debug failed'
+
+../../harmonization.py \
+--bvalMap 1000 \
+--resample 1.5x1.5x1.5 \
+--template ./template/ \
+--ref_list connectom.txt \
+--tar_list prisma.txt \
+--ref_name CONNECTOM \
+--tar_name PRISMA \
+--nproc -1 \
+--create --process --debug || EXIT 'harmonization.py with --create --process --debug failed'
+# ===============================================================================================================
+
+### Run pipeline and obtain statistics when small set of matched reference and target images are used in template creation
+### and a larger set (does not have to be mutually exclusive from the former) of target images are used in harmonization
+
+# test the following advanced parameter
+export TEMPLATE_CONSTRUCT_CORES=6
+
+# --create and --debug block
+../../harmonization.py \
+--bvalMap 1000 \
+--resample 1.5x1.5x1.5 \
+--template ./template/ \
+--ref_list connectom.txt \
+--tar_list prisma.txt \
+--ref_name CONNECTOM \
+--tar_name PRISMA \
+--travelHeads \
+--nproc -1 \
+--create --debug --force || EXIT 'harmonization.py with --create --debug --force failed'
+
+../../harmonization.py \
+--bvalMap 1000 \
+--resample 1.5x1.5x1.5 \
+--template ./template/ \
+--ref_list connectom.txt \
+--tar_list prisma.txt \
+--ref_name CONNECTOM \
+--tar_name PRISMA \
+--travelHeads \
+--nproc -1 \
+--create --debug || EXIT 'harmonization.py with --create --debug failed'
+
+# --process and --debug block
+../../harmonization.py \
+--bvalMap 1000 \
+--resample 1.5x1.5x1.5 \
+--template ./template/ \
+--tar_list prisma.txt \
+--tar_name PRISMA \
+--ref_list connectom.txt \
+--nproc -1 \
+--process --debug --force || EXIT 'harmonization.py with --process --debug --force failed'
+
+../../harmonization.py \
+--bvalMap 1000 \
+--resample 1.5x1.5x1.5 \
+--template ./template/ \
+--tar_list prisma.txt \
+--tar_name PRISMA \
+--ref_list connectom.txt \
+--nproc -1 \
+--process --debug || EXIT 'harmonization.py with --process --debug failed'
+
+# ===============================================================================================================
+
+# same bvalue, resolution block
+cp connectom.txt.modified connectom_same.txt
+cp prisma.txt.modified prisma_same.txt
+../../harmonization.py \
+--template ./template/ \
+--ref_list connectom_same.txt \
+--tar_list prisma_same.txt \
+--ref_name CONNECTOM \
+--tar_name PRISMA \
+--nproc -1 \
+--create --process || EXIT 'harmonization.py for same bvalue, resolution with --create --process failed'
+
+# ===============================================================================================================
+# compute statistics
+../fa_skeleton_test.py -i connectom.txt.modified \
+-s CONNECTOM -t template/ || EXIT 'fa_skeleton_test.py failed for modified reference'
+
+../fa_skeleton_test.py -i prisma.txt \
+-s PRISMA -t template/ || EXIT 'fa_skeleton_test.py failed for given target'
+
+../fa_skeleton_test.py -i prisma.txt.modified.harmonized \
+-s PRISMA -t template/ || EXIT 'fa_skeleton_test.py failed for harmonized target'
+
+# ===============================================================================================================
+
+