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Add set -eu for guarding against errors, allow vars to be set in the environment #3

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merged 1 commit into from
Jun 23, 2017
Merged

Add set -eu for guarding against errors, allow vars to be set in the environment #3

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19 changes: 12 additions & 7 deletions batch.sh
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Original file line number Diff line number Diff line change
@@ -1,5 +1,8 @@
#!/bin/bash

# Fail if anything not planed to go wrong, goes wrong
set -eu

# Test if command exists.
exists() {
test -x "$(command -v "$1")"
Expand All @@ -8,14 +11,16 @@ exists() {
#exenam is executable
# we assume it is in the users path
# however, this could be set explicitly, e.g.
# exenam="/Users/rorden/Documents/cocoa/dcm2niix/console/dcm2niix"
exenam="dcm2niix"
# exenam="/Users/rorden/Documents/cocoa/dcm2niix/console/dcm2niix" batch.sh
exenam=${examnam:-dcm2niix}

#basedir is folder with "Ref" and "In" subfolders.
# we assume it is the same same folder as the script
# however, this could be set explicitly, e.g.
# basedir="/Users/rorden/dcm_qa"
basedir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
# basedir="/Users/rorden/dcm_qa" batch.sh
if [ -z ${basedir:-} ]; then
basedir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
fi

#### no need to edit subsequent lines

Expand All @@ -31,17 +36,17 @@ exists $exenam ||
exit 1
}

if [ ! -d $indir ]; then
if [ ! -d "$indir" ]; then
echo "Error: Unable to find $indir"
exit 1
fi

if [ ! -d $refdir ]; then
if [ ! -d "$refdir" ]; then
echo "Error: Unable to find $refdir"
exit 1
fi

if [ ! -d $outdir ]; then
if [ ! -d "$outdir" ]; then
mkdir $outdir
fi

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