[Swift-commit] r3122 - in SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis: . chisqperm

[noreply at svn.ci.uchicago.edu]

Author: andric
Date: 2009-10-08 12:07:08 -0500 (Thu, 08 Oct 2009)
New Revision: 3122

Added:
   SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/
   SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/clustermassPerms2.swift
   SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/swift_ex.sh
Log:
seperate dir for chisq perms

Added: SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/clustermassPerms2.swift
===================================================================
--- SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/clustermassPerms2.swift	                        (rev 0)
+++ SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/clustermassPerms2.swift	2009-10-08 17:07:08 UTC (rev 3122)
@@ -0,0 +1,66 @@
+##-- coded: 13.Sept.2009
+type file{}
+type Rscript;
+
+## generate permutation brain
+app (external permOUT) permJob (Rscript code, string permOUTname){
+    RInvoke @code permOUTname;
+}
+
+## smooth the permutation brain
+app (external surfsmoothOutfile) SurfSmooth (file spec, file smoothwm, external permOUT, string surfsmoothOutfilename){
+    SurfSmooth "-spec" @spec "-surf_A" @smoothwm "-met" "HEAT_07" "-input" @permOUT
+    "-fwhm" 4 "-Niter" "-1" "-add_index" "-output" surfsmoothOutfilename;
+}
+
+## cluster the smoothed permutation brain
+app (external surfclustOutput) SurfClust (file spec, file pial, external 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, external surfclustOutput){
+    python @ClstrMassScript "--input" @filename(surfclustOutput) "--outputname" @filename(clusterMassOUT) "--procedure" "PermClusterMass";
+}
+
+(external permOUT, external surfsmoothOutfile, external surfclustOutput, file clusterMassOUT) PermClusterMass (Rscript code, file ClstrMassScript, file spec, file smoothwm, file pial, float thresh, float rmm, string outPrefix, string permOUTname, string surfsmoothOutfilename){
+    permOUT = permJob(code, permOUTname);
+    surfsmoothOutfile = SurfSmooth(spec, smoothwm, permOUT, surfsmoothOutfilename);
+    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{
+                external permOUT;
+                string permOUTname=@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);
+                external surfsmoothOutfile;
+                string surfsmoothOutfilename=@strcat(outPrefix,"smooth.1D.dset");
+                external surfclustOutput;
+                #string surfclustOutputname=@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, permOUTname, surfsmoothOutfilename);
+            }
+        }
+    }
+}

Added: SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/swift_ex.sh
===================================================================
--- SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/swift_ex.sh	                        (rev 0)
+++ SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/swift_ex.sh	2009-10-08 17:07:08 UTC (rev 3122)
@@ -0,0 +1,3 @@
+#!/bin/tcsh
+
+swift clstnodes.swift -sites.file /ci/projects/cnari/config/coaster_mercury.xml -user="andric"


Property changes on: SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/swift_ex.sh
___________________________________________________________________
Name: svn:executable
   + *