From fe3cd408d0a2291651acd17528d78bb79c39d26e Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Mon, 15 Jun 2015 10:45:13 +0000
Subject: [PATCH] Pythonised version
---
fsladd | 64 ++++++++++++++++++++++++++++++++--------------------------
1 file changed, 35 insertions(+), 29 deletions(-)
diff --git a/fsladd b/fsladd
index b36fda9..053bd5d 100755
--- a/fsladd
+++ b/fsladd
@@ -1,31 +1,37 @@
-#!/bin/sh
-# Copyright (C) 2012 University of Oxford
-#
-# SHCOPYRIGHT
+#!/usr/bin/env python
+# fsladd - add ( or average! ) a list of images
+# Stephen Smith, Saad Jbabdi and Matthew Webster FMRIB Image Analysis Group
+# Copyright (C) 2015 University of Oxford
+# SHBASECOPYRIGHT
+import sys
+import os
+import subprocess
+import argparse
-if [ "$1" == "" ];then
- echo ""
- echo "Usage: fsladd <output> [-m] <listOfVolumes> "
- echo ""
- echo "-m : calculates the mean instead of sum"
- echo ""
- exit 1
-fi
-
-o=$1
-shift;
-
-m=""
-if [ "$1" == "-m" ];then
- shift;
- m=" -div $#"
-fi
-
-cmd="${FSLDIR}/bin/fslmaths $1"
-shift;
-for i in $@;do
- cmd=" $cmd -add $i"
-done
-cmd=" $cmd $m $o"
-$cmd
+def main(output,files,scale,mean):
+ if scale:
+ newMean=1000
+ scales = [ newMean/float(subprocess.check_output([os.path.join(os.environ["FSLDIR"],"bin","fslstats"),inputFile,"-M"])) for inputFile in files ]
+ files = [ [files[i],"-mul",str(scales[i]/scales[i+1])] if i < len(scales)-1 else [files[i],"-mul",str(scales[i])] for i in range(0,len(scales)) ]
+ else:
+ files = [ [fileName] for fileName in files ]
+ command = [os.path.join(os.environ["FSLDIR"],"bin","fslmaths")]+files[0]
+ for index in range(1,len(files)):
+ command+=["-add"]+files[index]
+ if mean:
+ command+=["-div",str(len(files))]
+ command.append(output)
+ print command
+ status=subprocess.call(command)
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser(add_help=False,usage='%(prog)s <output> [-m] [-s] <listOfVolumes>')
+ parser.add_argument('-m',dest='mean',help='calculate mean instead of sum',action='store_true',default = False)
+ parser.add_argument('-s',dest='scale',help='scale each input image mean to 1000 before processing',action='store_true',default = False)
+ parser.add_argument('files',nargs='+',help=argparse.SUPPRESS)
+ if len(sys.argv) < 3:
+ parser.print_help()
+ sys.exit(1)
+ args=parser.parse_args(sys.argv[2:])
+ main(sys.argv[1],args.files,args.scale,args.mean)
--
GitLab