[Swift-commit] r2839 - in SwiftApps/SIDGrid/swift/swift_scripts: . sem

[noreply at svn.ci.uchicago.edu]

Author: skenny
Date: 2009-04-07 21:29:39 -0500 (Tue, 07 Apr 2009)
New Revision: 2839

Added:
   SwiftApps/SIDGrid/swift/swift_scripts/sem/
   SwiftApps/SIDGrid/swift/swift_scripts/sem/sem_demo.swift
Log:
prototype for frontiers paper

Added: SwiftApps/SIDGrid/swift/swift_scripts/sem/sem_demo.swift
===================================================================
--- SwiftApps/SIDGrid/swift/swift_scripts/sem/sem_demo.swift	                        (rev 0)
+++ SwiftApps/SIDGrid/swift/swift_scripts/sem/sem_demo.swift	2009-04-08 02:29:39 UTC (rev 2839)
@@ -0,0 +1,87 @@
+type file;
+type mxMin;
+type Rscript;
+type dbConnect;
+type mxModel{
+int modnum;
+int dof;
+string best;
+}
+# -------------- atomic procedures -------------- #
+
+(file matrix) runQuery (dbConnect dbconn, string query, Rscript calcCov){
+app{
+mysqlPythonAPI query @calcCov @dbconn;
+}
+}
+
+(external inserted) insertMxResult (dbConnect dbconn, string query, file datafile){
+app{
+mysqlPythonAPI query @dbconn stdout=@filename(inserted) @datafile;
+}
+}
+
+(file min) mxModelProcessor ( file cov, Rscript mxModProc, int modnum, float weight, string cond, int net){
+app{
+RInvoke @mxModProc @filename(cov) modnum weight cond net;
+}
+}
+
+# ------------ SEM user-defined procedures --------------- #
+
+multiNetworkSEM(string condition,dbConnect emblemdb, dbConnect semdb, int n, string net, int totalperms[]){
+float initweight = .75;
+file covariance<single_file_mapper;file=@strcat("matrices/net",n,"/",condition,".cov")>;
+covariance = getCovariance(condition, n, net, emblemdb);
+Rscript mxModProc<single_file_mapper;file="scripts/singlemodels.R">;
+foreach perm in totalperms{
+file modmin<single_file_mapper;file=@strcat("results/net",n,"/",condition,"_",perm,".stat")>;
+modmin =  mxModelProcessor(covariance,mxModProc,perm,initweight,condition,n);
+external doneflag = insertOptMod(n, semdb, condition, modmin);
+
+}
+
+(external ins) insertOptMod(int net, dbConnect dbconn, string cond, file modfile){
+string mysqlstr = @strcat("INSERT INTO optimized_models (network,deg_of_freedom,mx_minimum, modnum, cond) VALUES (",net,",DOF,BEST,MODNUM,",cond,");");
+string argList = @strcat(
+" --query ", mysqlstr,
+" --data ", @filename(modfile),
+" --conf ", @filename(dbconn));
+ins = insertMxResult(dbconn, argList, modfile);
+}
+
+(file covariance) getCovariance (string cond, int net, string rois, dbConnect dbconn){
+string mysqlstr = @strcat("SELECT avg(",cond,"0B), avg(",cond,"1B), avg(",cond,"2B),",
+"avg(",cond,"3B), avg(",cond,"4B), avg(",cond,"5B),",
+"avg(",cond,"6B), avg(",cond,"7B), avg(",cond,"8B) ",
+"FROM emblemfemlh where roi in (",rois,") group by roi ");
+string argList = @strcat(
+" --conf ", "user.config",
+" --query ", mysqlstr,
+" --r_script ", "scripts/cov.R",
+" --r_swift_args ", "matrices/net",net, "/", cond);
+Rscript calcCov<single_file_mapper;file="scripts/cov.R">;
+covariance = runQuery(dbconn, argList, calcCov);
+}
+
+(file plotfile) plotLogLik(int net, string cond, dbConnect dbconn){
+Rscript rplot<single_file_mapper;file="scripts/plotloglik.R">;
+string mysqlstr = @strcat("SELECT deg_of_freedom,mx_minimum FROM optimized_models",
+" where network = ",net,";");
+string argList = @strcat(
+" --conf ", @filename(dbconn),
+" --query ", mysqlstr,
+" --r_script ", "scripts/plotloglik.R",
+" --r_swift_args ", @filename(plotfile));
+plotfile = runQuery(dbconn, argList, rplot);
+}# ----------------------- Main ------------------------ #
+
+
+string condition = "gestspeech";
+string networks[] = ["42, 34, 33, 60", "42, 15, 60, 80", "33, 34, 23, 80"];
+dbConnect emblemdb <single_file_mapper; file="./user.config">;
+dbConnect semdb <single_file_mapper; file="./user2.config">;
+int totalperms[] = [1:65536];
+foreach net,n in networks{
+multiNetworkSEM(condition,emblemdb,semdb,n,net);
+}