[Swift-commit] r6554 - SwiftTutorials/OHBM_2013-06-16

[wilde at ci.uchicago.edu]

Author: wilde
Date: 2013-06-14 16:27:01 -0500 (Fri, 14 Jun 2013)
New Revision: 6554

Modified:
   SwiftTutorials/OHBM_2013-06-16/genatlas.swift
Log:
Adjust names for align()

Modified: SwiftTutorials/OHBM_2013-06-16/genatlas.swift
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/genatlas.swift	2013-06-14 21:19:57 UTC (rev 6553)
+++ SwiftTutorials/OHBM_2013-06-16/genatlas.swift	2013-06-14 21:27:01 UTC (rev 6554)
@@ -45,13 +45,12 @@
 
 # start of genatlas workflow
 
-file   alignScript<"align.sh">;
-  /* This script does:
-  time $AIR5/bin/alignlinear $ref $anat init.warp \
+file   alignScript<"align.sh">;  /* This script does:
+   alignlinear $ref $anat init.warp \
     -m 15 -t1 55 -t2 55 -x 1 -r 8 -c 0.1 -h 8 
-  time $AIR5/bin/align_warp  $ref $anat refined.warp \
-    -m 1 12 -b1 .1 .1 .1  -b2 .1 .1 .1 -f init.warp -h 10000 -s 1024 2 2 -c .01 # -v -q -s 1024 2 2 -c .01
-  time $AIR5/bin/reslice refined.warp $resliced -a $anat
+  align_warp  $ref $anat refined.warp \
+    -m 1 12 -b1 .1 .1 .1  -b2 .1 .1 .1 -f init.warp -h 10000 -s 1024 2 2 -c .01
+  reslice refined.warp $resliced -a $anat
   */
 
 app (Volume alignedVol) align_sh (file script, Volume reference, Volume input)
@@ -59,7 +58,7 @@
   sh @script @filename(reference.image) @filename(input.image) @filename(alignedVol.image);
 }
 
-(Volume alignedVol) native_align (Volume ref, Volume subject)
+(Volume alignedVol) align (Volume ref, Volume subject)
 {
   file firstwarp = alignlinear(ref, subject,
                      ["-m","15","-t1","55","-t2","55","-x","1","-r","8","-c","0.1","-h","8"]);
@@ -80,8 +79,8 @@
 
 foreach v, i in inputVolumes {
   Volume aligned<ext; exec="volmapper",name=@strcat("work/aligned",i)>;
-  // aligned = align(alignScript,referenceVolume, v);
-  aligned = native_align(referenceVolume, v);
+  // aligned = align_sh(alignScript,referenceVolume, v);
+  aligned = align(referenceVolume, v);
   outputVolumes[i] = aligned;
 }
 
@@ -100,9 +99,6 @@
 
 
 
-
-
-
 /******* The following code to be removed
 
 string testNames[] = imageNames(outputVolumes);