[Swift-commit] r3040 - SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis

[noreply at svn.ci.uchicago.edu]

Author: andric
Date: 2009-08-05 15:59:17 -0500 (Wed, 05 Aug 2009)
New Revision: 3040

Added:
   SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/turning.swift
Log:
swift script to do turnpoints analysis

Added: SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/turning.swift
===================================================================
--- SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/turning.swift	                        (rev 0)
+++ SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/turnpointAnalysis/turning.swift	2009-08-05 20:59:17 UTC (rev 3040)
@@ -0,0 +1,48 @@
+#--- turnpoints across the brain via Mediator - for PK2
+## type declarations:
+type file{}
+type Rscript;
+## a type for simple mapping the two output files:
+
+## Mediator app declaration:
+app (file tarOut) run_query (string med_args, file config, Rscript code, file Annot){
+    Mediator med_args @filename(code) @filename(Annot);
+}
+
+## this process sets parameters and calls Mediator:
+loop_query(int vert, string user, string db, string host, string query_outline, Rscript code, file config, string subject, string h, int beginTS, int endTS, file Annot){
+    string outPrefix = @strcat("pa_vs_noise_vert",vert,h);
+    string tarPrefix = @strcat("turning_out",h,"/vert",vert,"_",h);
+    file tarOut<single_file_mapper; file=@strcat(tarPrefix,".tgz")>;
+    string med_args = @strcat("--user ","andric"," --conf ", @filename(config)," --db ", db," --host ", host,
+        " --vox ", vert," --subject ", subject," --subquery tsTSVAR"," --begin_ts ",beginTS," --end_ts ",endTS,
+        " --query ", query_outline," --r_swift_args ",outPrefix," ",vert," ",h," ", at filename(tarOut), " --outprefix ", "FAH_Q", " --r_script ", at filename(code));
+    (tarOut) = run_query(med_args, config, code, Annot);
+}
+
+## needed parameters to use Mediator:
+string user = @arg("user");
+string db = "HEL";
+string host = "tp-neurodb.ci.uchicago.edu";
+file config<single_file_mapper; file="user.config">;
+
+## mapping the R code:
+Rscript code<single_file_mapper; file="Rturning/turnchi.R">;
+file Annot<single_file_mapper; file="Rturning/for3dDecon.PK2_4condSHORTcat_all.1D">;
+
+## variables to move across in the foreach loops:
+string declarelist[] = ["PK2smth"];
+string hemilist[] = ["lh"];
+int vertices[] = [0:130933:1];
+#int vertices[] = [0:1:1];
+
+foreach subject in declarelist{
+    foreach h in hemilist{
+        int beginTS = 0;
+        int endTS = 1807;
+        string query_outline = @strcat("SELECT SUBQUERY FROM peakTS_data",h," WHERE subject = '",subject,"' AND vertex=VOX");
+        foreach vert in vertices{
+            loop_query(vert, user, db, host, query_outline, code, config, subject, h, beginTS, endTS, Annot);
+        }
+    }
+}