[Swift-commit] r3111 - SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/permutations

[noreply at svn.ci.uchicago.edu]

Author: andric
Date: 2009-09-21 12:05:37 -0500 (Mon, 21 Sep 2009)
New Revision: 3111

Added:
   SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/permutations/clustermassPerms.swift
Log:
swift script for doing surface alphasim

Added: SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/permutations/clustermassPerms.swift
===================================================================
--- SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/permutations/clustermassPerms.swift	                        (rev 0)
+++ SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/permutations/clustermassPerms.swift	2009-09-21 17:05:37 UTC (rev 3111)
@@ -0,0 +1,63 @@
+##-- coded: 13.Sept.2009
+type file{}
+type Rscript;
+
+## generate permutation brain
+app (file permOUT) permJob (Rscript code){
+    RInvoke @code @filename(permOUT);
+}
+
+## smooth the permutation brain
+app (file surfsmoothOutfile) SurfSmooth (file spec, file smoothwm, file permOUT){
+    SurfSmooth "-spec" @spec "-surf_A" @smoothwm "-met" "HEAT_07" "-input" @permOUT
+    "-fwhm" 4 "-Niter" "-1" "-add_index" "-output" @filename(surfsmoothOutfile);
+}
+
+## cluster the smoothed permutation brain
+app (file surfclustOutput) SurfClust (file spec, file pial, file surfsmoothOutfile, float thresh, float rmm, string outPrefix){
+        SurfClust "-spec" @spec "-surf_A" @pial "-input" @surfsmoothOutfile "1" "-rmm" rmm "-thresh_col" "1"
+        "-thresh" thresh "-amm2" "2" "-sort_n_nodes" "-prepend_node_index" "-prefix" outPrefix;
+}
+
+## calculate the cluster mass and keep the biggest one
+app (file clusterMassOUT) ClusterMass (file ClstrMassScript, file surfclustOutput){
+    python @ClstrMassScript "--input" @filename(surfclustOutput) "--outputname" @filename(clusterMassOUT) "--procedure" "PermClusterMass";
+}
+
+(file permOUT, file surfsmoothOutfile, file surfclustOutput, file clusterMassOUT) PermClusterMass (Rscript code, file ClstrMassScript, file spec, file smoothwm, file pial, float thresh, float rmm, string outPrefix){
+    permOUT = permJob(code);
+    surfsmoothOutfile = SurfSmooth(spec, smoothwm, permOUT);
+    surfclustOutput = SurfClust(spec, pial, surfsmoothOutfile, thresh, rmm, outPrefix);
+    clusterMassOUT = ClusterMass(ClstrMassScript, surfclustOutput);
+}
+
+
+Rscript code<single_file_mapper; file="scripts/generatePerm.R">;
+file ClstrMassScript<single_file_mapper; file="ClstrMasstr.py">;
+
+string idss[] = ["pa_vs_noise"];
+string way = "oneway";
+int lag = 0;
+string h = "lh";
+float vertexThresh[] = [3.84];
+float rmm_vals[] = [3.1];
+#int permbrains[] = [1:1000:1];
+int permbrains[] = [1];
+
+foreach id in idss{
+    foreach perm in permbrains{
+        foreach thresh in vertexThresh{
+            foreach rmm in rmm_vals{
+                file permOUT<single_file_mapper; file=@strcat("perm",perm,".1D")>;
+                file spec<single_file_mapper;file=@strcat("PK2_",h,".spec")>;
+                file smoothwm<single_file_mapper; file=@strcat(h,".smoothwm.asc")>;
+                file pial<single_file_mapper;file=@strcat(h,".pial.asc")>;
+                string outPrefix=@strcat("perm",perm,id,"_",h,"_lag",lag,way,"Thresh",thresh);
+                file surfsmoothOutfile<single_file_mapper; file=@strcat(outPrefix,"smooth.1D.dset")>;
+                file surfclustOutput<single_file_mapper; file=@strcat(outPrefix,"_ClstTable_r",rmm,"_a2.0.1D")>;
+                file clusterMassOUT<single_file_mapper; file=@strcat("perm",perm,id,"_",h,"_lag",lag,way,"_r",rmm,"Thresh",thresh,"PERMMASS.txt")>;
+                (permOUT, surfsmoothOutfile, surfclustOutput, clusterMassOUT) = PermClusterMass(code, ClstrMassScript, spec, smoothwm, pial, thresh, rmm, outPrefix);
+            }
+        }
+    }
+}