[Swift-commit] r3156 - SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm

[noreply at svn.ci.uchicago.edu]

Author: andric
Date: 2009-10-13 12:23:14 -0500 (Tue, 13 Oct 2009)
New Revision: 3156

Added:
   SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/alphasurfsim2.swift
Log:
doing alphasurfsim via swift

Added: SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/alphasurfsim2.swift
===================================================================
--- SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/alphasurfsim2.swift	                        (rev 0)
+++ SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/chisqperm/alphasurfsim2.swift	2009-10-13 17:23:14 UTC (rev 3156)
@@ -0,0 +1,30 @@
+## pinche AlphaSim surface style
+type file{}
+type Rscript;
+
+app (file clusterResult) AlphaSurfSim (file Alphasurf, Rscript code, string permOut, file spec, file smoothwm, file pial, string smoothout, string maskout, float rmm, string surfclustout, string inputclustout){
+    python @Alphasurf "--r_script" @code "--permOut" permOut  "--spec" @spec "--smoothwm" @smoothwm "--pial" @pial "--surfsmoothOut" smoothout "--maskname" maskout "--rmm" rmm "--pval" 0.05 "--surfclustOut" surfclustout "--proc_input" inputclustout "--procedure" "PermNumberNodes" "--outputname" @filename(clusterResult);
+}
+
+file Alphasurf<single_file_mapper; file="Alphasurfsim.py">;
+Rscript code<single_file_mapper; file="fahQchsq.R">;
+
+string h = "lh";
+float rmm_vals[] = [3.1];
+int permbrains[] = [1:1000];
+#int permbrains[] = [1:2];
+
+foreach perm in permbrains{
+    foreach rmm in rmm_vals{
+        string permOut = @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 smoothout = @strcat("perm",perm,"_",h,"smooth.1D.dset");
+        string maskout = @strcat("perm",perm,"_",h,"smoothmask.1D");
+        string surfclustout = @strcat("perm",perm,"_",h,"clustout");
+        string inputclustout = @strcat("perm",perm,"_",h,"clustout_ClstTable_r",rmm,"_a2.0.1D");
+        file clusterResult<single_file_mapper; file=@strcat("perm",perm,"_",h,"rmm",rmm,"nnodes.txt")>;
+        clusterResult = AlphaSurfSim(Alphasurf, code, permOut, spec, smoothwm, pial, smoothout, maskout, rmm, surfclustout, inputclustout);
+    }
+}