[Swift-commit] r3081 - SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations
noreply at svn.ci.uchicago.edu
noreply at svn.ci.uchicago.edu
Sat Aug 8 10:36:17 CDT 2009
Author: andric
Date: 2009-08-08 10:36:17 -0500 (Sat, 08 Aug 2009)
New Revision: 3081
Added:
SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/PermFriedman.swift
SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/PermFriedman1001.swift
SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/PermFriedman2001.swift
SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/oldPermFriedman.swift
SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/permclust.swift
SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/permclustThresh6.swift
SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/permclustnotnew.swift
Log:
SwiftScripts for permutations and clustering
Added: SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/PermFriedman.swift
===================================================================
--- SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/PermFriedman.swift (rev 0)
+++ SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/PermFriedman.swift 2009-08-08 15:36:17 UTC (rev 3081)
@@ -0,0 +1,53 @@
+#---- coded Tuesday; July 22, 2008
+type file{}
+
+(file qout, file rout) run_query (string allcatargs, file config, file r_script, file r_config_conds, file r_config_subjs){
+ app{
+ Mediator allcatargs stdout=@filename(qout) @filename(r_script) @filename(r_config_conds) @filename(r_config_subjs);
+ }
+}
+
+string user = @arg("user");
+string db = "EMBLEM1";
+string host = "tp-neurodb.ci.uchicago.edu";
+#string host = "login4.ranger.tacc.utexas.edu";
+
+file r_script<single_file_mapper; file="scripts/NewPermFriedman.R">;
+file r_config_conds<single_file_mapper; file="config_file.Rdata">;
+file r_config_subjs<single_file_mapper; file="subjs_config_file.txt">;
+file config<single_file_mapper; file="user.config">;
+
+
+loop_query(int bvox, string user, string db, string host, string query_outline, file r_script, file config, file r_config_conds, file r_config_subjs, string id, int medstep, int swiftstep){
+ int evox = bvox+(swiftstep-1);
+ string baseid = "PermFriedman";
+ string r_swift_args = @strcat(id);
+ string theoutprefix = @strcat(id,baseid,bvox,"_",evox);
+ string med_args = @strcat("--user ",user,
+ " --conf ", "user.config",
+ " --db ", db,
+ " --host ", host,
+ " --query ", query_outline,
+ " --r_script ", @filename(r_script),
+ " --begin_vox ", bvox,
+ " --end_vox ", evox,
+ " --outprefix ", theoutprefix,
+ " --batchstep ", medstep,
+ " --r_swift_args ", r_swift_args,
+ " --subject ", id);
+ file q_result <single_file_mapper; file=@strcat("query_results/",theoutprefix,".qresult")>;
+ file r_result <single_file_mapper; file=@strcat(theoutprefix,".tar")>;
+ (q_result, r_result) = run_query(med_args, r_script, config, r_config_conds, r_config_subjs);
+}
+
+int swiftstep = 28000;
+int mediatorstep = 7000;
+int permbrains = [1:1000:1];
+foreach perm in permbrains {
+ int mybatches = [1:196000:swiftstep];
+ foreach batch in mybatches {
+ string id = @strcat(perm);
+ string query_outline = @strcat("select subject, vertex, speech_lag, emblem_lag, embspeech_lag from ccf_phase2_lh where vertex between BEGIN_BATCH and END_BATCH");
+ loop_query(batch, user, db, host, query_outline, r_script, config, r_config_conds, r_config_subjs, id, mediatorstep, swiftstep);
+ }
+}
Added: SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/PermFriedman1001.swift
===================================================================
--- SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/PermFriedman1001.swift (rev 0)
+++ SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/PermFriedman1001.swift 2009-08-08 15:36:17 UTC (rev 3081)
@@ -0,0 +1,53 @@
+#---- coded Tuesday; July 22, 2008
+type file{}
+
+(file qout, file rout) run_query (string allcatargs, file config, file r_script, file r_config_conds, file r_config_subjs){
+ app{
+ Mediator allcatargs stdout=@filename(qout) @filename(r_script) @filename(r_config_conds) @filename(r_config_subjs);
+ }
+}
+
+string user = @arg("user");
+string db = "EMBLEM1";
+string host = "tp-neurodb.ci.uchicago.edu";
+#string host = "login4.ranger.tacc.utexas.edu";
+
+file r_script<single_file_mapper; file="scripts/NewPermFriedman.R">;
+file r_config_conds<single_file_mapper; file="config_file.Rdata">;
+file r_config_subjs<single_file_mapper; file="subjs_config_file.txt">;
+file config<single_file_mapper; file="user.config">;
+
+
+loop_query(int bvox, string user, string db, string host, string query_outline, file r_script, file config, file r_config_conds, file r_config_subjs, string id, int medstep, int swiftstep){
+ int evox = bvox+(swiftstep-1);
+ string baseid = "PermFriedman";
+ string r_swift_args = @strcat(id);
+ string theoutprefix = @strcat(id,baseid,bvox,"_",evox);
+ string med_args = @strcat("--user ",user,
+ " --conf ", "user.config",
+ " --db ", db,
+ " --host ", host,
+ " --query ", query_outline,
+ " --r_script ", @filename(r_script),
+ " --begin_vox ", bvox,
+ " --end_vox ", evox,
+ " --outprefix ", theoutprefix,
+ " --batchstep ", medstep,
+ " --r_swift_args ", r_swift_args,
+ " --subject ", id);
+ file q_result <single_file_mapper; file=@strcat("query_results/",theoutprefix,".qresult")>;
+ file r_result <single_file_mapper; file=@strcat(theoutprefix,".tar")>;
+ (q_result, r_result) = run_query(med_args, r_script, config, r_config_conds, r_config_subjs);
+}
+
+int swiftstep = 28000;
+int mediatorstep = 7000;
+int permbrains = [1001:2000:1];
+foreach perm in permbrains {
+ int mybatches = [1:196000:swiftstep];
+ foreach batch in mybatches {
+ string id = @strcat(perm);
+ string query_outline = @strcat("select subject, vertex, speech_lag, emblem_lag, embspeech_lag from ccf_phase2_lh where vertex between BEGIN_BATCH and END_BATCH");
+ loop_query(batch, user, db, host, query_outline, r_script, config, r_config_conds, r_config_subjs, id, mediatorstep, swiftstep);
+ }
+}
Added: SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/PermFriedman2001.swift
===================================================================
--- SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/PermFriedman2001.swift (rev 0)
+++ SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/PermFriedman2001.swift 2009-08-08 15:36:17 UTC (rev 3081)
@@ -0,0 +1,53 @@
+#---- coded Tuesday; July 22, 2008
+type file{}
+
+(file qout, file rout) run_query (string allcatargs, file config, file r_script, file r_config_conds, file r_config_subjs){
+ app{
+ Mediator allcatargs stdout=@filename(qout) @filename(r_script) @filename(r_config_conds) @filename(r_config_subjs);
+ }
+}
+
+string user = @arg("user");
+string db = "EMBLEM1";
+string host = "tp-neurodb.ci.uchicago.edu";
+#string host = "login4.ranger.tacc.utexas.edu";
+
+file r_script<single_file_mapper; file="scripts/NewPermFriedman.R">;
+file r_config_conds<single_file_mapper; file="config_file.Rdata">;
+file r_config_subjs<single_file_mapper; file="subjs_config_file.txt">;
+file config<single_file_mapper; file="user.config">;
+
+
+loop_query(int bvox, string user, string db, string host, string query_outline, file r_script, file config, file r_config_conds, file r_config_subjs, string id, int medstep, int swiftstep){
+ int evox = bvox+(swiftstep-1);
+ string baseid = "PermFriedman";
+ string r_swift_args = @strcat(id);
+ string theoutprefix = @strcat(id,baseid,bvox,"_",evox);
+ string med_args = @strcat("--user ",user,
+ " --conf ", "user.config",
+ " --db ", db,
+ " --host ", host,
+ " --query ", query_outline,
+ " --r_script ", @filename(r_script),
+ " --begin_vox ", bvox,
+ " --end_vox ", evox,
+ " --outprefix ", theoutprefix,
+ " --batchstep ", medstep,
+ " --r_swift_args ", r_swift_args,
+ " --subject ", id);
+ file q_result <single_file_mapper; file=@strcat("query_results/",theoutprefix,".qresult")>;
+ file r_result <single_file_mapper; file=@strcat(theoutprefix,".tar")>;
+ (q_result, r_result) = run_query(med_args, r_script, config, r_config_conds, r_config_subjs);
+}
+
+int swiftstep = 28000;
+int mediatorstep = 7000;
+int permbrains = [2001:3000:1];
+foreach perm in permbrains {
+ int mybatches = [1:196000:swiftstep];
+ foreach batch in mybatches {
+ string id = @strcat(perm);
+ string query_outline = @strcat("select subject, vertex, speech_lag, emblem_lag, embspeech_lag from ccf_phase2_lh where vertex between BEGIN_BATCH and END_BATCH");
+ loop_query(batch, user, db, host, query_outline, r_script, config, r_config_conds, r_config_subjs, id, mediatorstep, swiftstep);
+ }
+}
Added: SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/oldPermFriedman.swift
===================================================================
--- SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/oldPermFriedman.swift (rev 0)
+++ SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/oldPermFriedman.swift 2009-08-08 15:36:17 UTC (rev 3081)
@@ -0,0 +1,54 @@
+#---- coded Tuesday; July 22, 2008
+type file{}
+
+(file qout, file rout) run_query (string allcatargs, file config, file r_script, file r_config_conds, file r_config_subjs){
+ app{
+ Mediator allcatargs stdout=@filename(qout) @filename(r_script) @filename(r_config_conds) @filename(r_config_subjs);
+ }
+}
+
+string user = @arg("user");
+string db = "EMBLEM1";
+string host = "tp-neurodb.ci.uchicago.edu";
+#string host = "login4.ranger.tacc.utexas.edu";
+
+file r_script<single_file_mapper; file="scripts/NewPermFriedman.R">;
+file r_config_conds<single_file_mapper; file="config_file.Rdata">;
+file r_config_subjs<single_file_mapper; file="subjs_config_file.txt">;
+file config<single_file_mapper; file="user.config">;
+
+
+loop_query(int bvox, string user, string db, string host, string query_outline, file r_script, file config, file r_config_conds, file r_config_subjs, string id, int medstep, int swiftstep){
+ int evox = bvox+(swiftstep-1);
+ int batch_evox = bvox+(medstep-1);
+ string baseid = "PermFriedman";
+ string r_swift_args = @strcat(id);
+ string theoutprefixR_result = @strcat(id,baseid,bvox,"_",batch_evox);
+ string theoutprefixQuery_result = @strcat(id,baseid,bvox,"_",evox);
+ string med_args = @strcat("--user ",user,
+ " --conf ", "user.config",
+ " --db ", db,
+ " --host ", host,
+ " --query ", query_outline,
+ " --r_script ", @filename(r_script),
+ " --begin_vox ", bvox,
+ " --end_vox ", evox,
+ " --batchstep ", medstep,
+ " --r_swift_args ", r_swift_args,
+ " --subject ", id);
+ file q_result <single_file_mapper; file=@strcat("query_results/",theoutprefixQuery_result,".qresult")>;
+ file r_result <single_file_mapper; file=@strcat(theoutprefixR_result,".txt")>;
+ (q_result, r_result) = run_query(med_args, r_script, config, r_config_conds, r_config_subjs);
+}
+
+int swiftstep = 28000;
+int mediatorstep =7000;
+int permbrains = [1:1:1];
+foreach perm in permbrains {
+ int mybatches = [1:196000:swiftstep];
+ foreach batch in mybatches {
+ string id = @strcat(perm);
+ string query_outline = @strcat("select subject, vertex, speech_lag, emblem_lag, embspeech_lag from ccf_phase2_lh where vertex between BEGIN_BATCH and END_BATCH");
+ loop_query(batch, user, db, host, query_outline, r_script, config, r_config_conds, r_config_subjs, id, mediatorstep, swiftstep);
+ }
+}
Added: SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/permclust.swift
===================================================================
--- SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/permclust.swift (rev 0)
+++ SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/permclust.swift 2009-08-08 15:36:17 UTC (rev 3081)
@@ -0,0 +1,33 @@
+# Tuesday; July 22, 2008
+# checked over and set again on Friday; August 22, 2008
+# this version loops also the rmm value
+type file{}
+
+type surfclust_table{}
+
+
+(surfclust_table surfclustOutput) SurfClust (file specFile, file surfFile, file input, int threshVal, float rmmVal, string prefix){
+ app {
+ SurfClust "-spec" @filename(specFile) "-surf_A" @filename(surfFile) "-input" @filename(input) "1" "-rmm" rmmVal "-thresh_col" "1" "-thresh" threshVal "-amm2" "2" "-sort_n_nodes" "-prepend_node_index" "-prefix" prefix;
+ }
+}
+
+
+int vertexThresh[] = [6,9];
+int permbrains[] = [3:3000:1];
+#int permbrains[] = [1:2:1];
+float rmm_vals[] = [2.2,2.5];
+
+foreach brain in permbrains{
+ foreach thresh in vertexThresh{
+ foreach rmm in rmm_vals{
+ file HORRYspec <single_file_mapper;file=@strcat("HORRY.rh.mesh140_std.spec")>;
+ file HORRYsurf <single_file_mapper;file=@strcat("HORRY.rh.mesh140_std.pial.asc")>;
+ string inputName=@strcat("PermBrain",brain,"_output.txt");
+ file inputFile <single_file_mapper;file=inputName>;
+ string outPrefix=@strcat(brain,"_Thresh",thresh);
+ surfclust_table surfclustOutput <single_file_mapper; file=@strcat(outPrefix,"_ClstTable_r",rmm,"_a2.0.1D")>;
+ (surfclustOutput) = SurfClust(HORRYspec,HORRYsurf,inputFile,thresh,rmm,outPrefix);
+ }
+ }
+}
Added: SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/permclustThresh6.swift
===================================================================
--- SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/permclustThresh6.swift (rev 0)
+++ SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/permclustThresh6.swift 2009-08-08 15:36:17 UTC (rev 3081)
@@ -0,0 +1,33 @@
+# Tuesday; July 22, 2008
+# checked over and set again on Friday; August 22, 2008
+# this version loops also the rmm value
+type file{}
+
+type surfclust_table{}
+
+
+(surfclust_table surfclustOutput) SurfClust (file specFile, file surfFile, file input, int threshVal, float rmmVal, string prefix){
+ app {
+ SurfClust "-spec" @filename(specFile) "-surf_A" @filename(surfFile) "-input" @filename(input) "1" "-rmm" rmmVal "-thresh_col" "1" "-thresh" threshVal "-amm2" "2" "-sort_n_nodes" "-prepend_node_index" "-prefix" prefix;
+ }
+}
+
+
+int vertexThresh[] = [6];
+int permbrains[] = [3:3000:1];
+#int permbrains[] = [1:2:1];
+float rmm_vals[] = [2.2,2.5];
+
+foreach brain in permbrains{
+ foreach thresh in vertexThresh{
+ foreach rmm in rmm_vals{
+ file HORRYspec <single_file_mapper;file=@strcat("HORRY.lh.mesh140_std.spec")>;
+ file HORRYsurf <single_file_mapper;file=@strcat("HORRY.lh.mesh140_std.pial.asc")>;
+ string inputName=@strcat("PermBrain",brain,"_output.txt");
+ file inputFile <single_file_mapper;file=inputName>;
+ string outPrefix=@strcat(brain,"_Thresh",thresh);
+ surfclust_table surfclustOutput <single_file_mapper; file=@strcat(outPrefix,"_ClstTable_r",rmm,"_a2.0.1D")>;
+ (surfclustOutput) = SurfClust(HORRYspec,HORRYsurf,inputFile,thresh,rmm,outPrefix);
+ }
+ }
+}
Added: SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/permclustnotnew.swift
===================================================================
--- SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/permclustnotnew.swift (rev 0)
+++ SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/NewPermutations/permclustnotnew.swift 2009-08-08 15:36:17 UTC (rev 3081)
@@ -0,0 +1,33 @@
+# coded Tuesday; July 22, 2008
+# checked over and set again on Friday; August 22, 2008
+# this version loops also the rmm value
+type file{}
+
+type surfclust_table{}
+
+
+(surfclust_table surfclustOutput) SurfClust (file specFile, file surfFile, file input, int threshVal, float rmmVal, string prefix){
+ app {
+ SurfClust "-spec" @filename(specFile) "-surf_A" @filename(surfFile) "-input" @filename(input) "1 -rmm" rmmVal "-thresh_col 1 -thresh" threshVal "-amm2 2 -sort_n_nodes -prepend_node_index -prefix" prefix;
+ }
+}
+
+
+int vertexThresh[] = [9];
+#int permbrains = [2001:3000:1];
+int permbrains = [1:2:1];
+float rmm_vals = [2.2,2.5];
+
+foreach brain in permbrains{
+ foreach thresh in vertexThresh{
+ foreach rmm in rmm_vals{
+ file HORRYspec <single_file_mapper;file=@strcat("HORRY.lh.mesh140_std.spec")>;
+ file HORRYsurf <single_file_mapper;file=@strcat("HORRY.lh.mesh140_std.pial.asc")>;
+ string inputName=@strcat("brain_",brain,"PermFriedman.txt");
+ file inputFile <single_file_mapper;file=inputName>;
+ string outPrefix=@strcat(brain,"_Thresh",thresh);
+ surfclust_table surfclustOutput <single_file_mapper; file=@strcat(outPrefix,"_ClstTable_r",rmm,"_a2.0.1D")>;
+ (surfclustOutput) = SurfClust(HORRYspec,HORRYsurf,inputFile,thresh,rmm,outPrefix);
+ }
+ }
+}
More information about the Swift-commit
mailing list