[Swift-commit] r2110 - SwiftApps/SIDGrid/swift/projects/skenny/openmx

[noreply at svn.ci.uchicago.edu]

Author: skenny
Date: 2008-07-10 13:28:07 -0500 (Thu, 10 Jul 2008)
New Revision: 2110

Added:
   SwiftApps/SIDGrid/swift/projects/skenny/openmx/modelproc.swift
Log:
runs RAM model for mx model on the previosly generated mx models

Added: SwiftApps/SIDGrid/swift/projects/skenny/openmx/modelproc.swift
===================================================================
--- SwiftApps/SIDGrid/swift/projects/skenny/openmx/modelproc.swift	                        (rev 0)
+++ SwiftApps/SIDGrid/swift/projects/skenny/openmx/modelproc.swift	2008-07-10 18:28:07 UTC (rev 2110)
@@ -0,0 +1,57 @@
+type file{}
+
+# query database for timeseries data and pass to 
+# R script to calculate observed covariance and
+# run model (RAM)
+
+(file fitmodel, file func_value) simple_covariance (string allcatargs, file config, file dot_r, file mxmodel){
+    app{
+        Mediator allcatargs @filename(dot_r) @filename(mxmodel);
+    }
+}
+
+model_data(string query, string cond, int modnum, file r_script){
+	file pmod<single_file_mapper; file=@strcat("modelObjects/",modnum,"_model.rdata")>;
+	string db = "EMBLEM1";
+	string host = "tp-neurodb.ci.uchicago.edu";
+	file config<single_file_mapper; file="user.config">;
+	string user = @arg("user");
+	string r_swift_args = @strcat(modnum,"_model.rdata");
+	string med_args = @strcat("--user ", user,
+    		" --conf ", @filename(config),
+    		" --db ", db,
+    		" --host ", host,
+    		" --query ", query,
+    		" --r_script ", @filename(r_script),
+    		" --r_swift_args ", r_swift_args,
+    		" --begin_vox ", 1,
+		" --end_vox ", 2,
+		" --batchstep ", 1,
+		" --outprefix ", @strcat(modnum,"_modeldata"),
+    		" --subject ", "model");
+	file resmod <single_file_mapper; file=@strcat(cond,"/",modnum,"/","model.rdata")>;
+	file modmin <single_file_mapper;file=@strcat(cond,"/",modnum,"/","function.min")>;
+	(resmod, modmin) = simple_covariance(med_args, config, r_script, pmod);
+}
+
+#............................main................................................
+
+# generate queries based on condition and roi's
+
+string conditions = ["gestspeech", "speech", "gesture", "grasp"];
+string queries[];
+foreach cond,c in conditions{
+	queries[c] = @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 = 42 or roi = 34 or roi = 33 or roi = 60 group by roi;");	
+}
+
+file cov_script<single_file_mapper; file="scripts/SimpleCovariance.R">;
+
+int models = [1:2];
+
+foreach m in models{
+	foreach query,q in queries {
+		model_data(query,conditions[q],m,cov_script);
+		}
+	    }
+
+