From 84b6c1840fd55940b2bc442c7a3e7cd5b214950f Mon Sep 17 00:00:00 2001
From: Moises Fernandez <moisesf@fmrib.ox.ac.uk>
Date: Fri, 12 Apr 2013 14:27:59 +0000
Subject: [PATCH] Method to merge the result parts of Bedpostx. Call from
post-proc script
---
merge_parts_gpu.cc | 141 +++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 141 insertions(+)
create mode 100644 merge_parts_gpu.cc
diff --git a/merge_parts_gpu.cc b/merge_parts_gpu.cc
new file mode 100644
index 0000000..35eaa00
--- /dev/null
+++ b/merge_parts_gpu.cc
@@ -0,0 +1,141 @@
+/* merge_parts_gpu.cc
+
+ Tim Behrens, Saad Jbabdi, Stam Sotiropoulos, Moises Hernandez - FMRIB Image Analysis Group
+
+ Copyright (C) 2005 University of Oxford */
+
+/* CCOPYRIGHT */
+
+#include "xfibresoptions.h"
+#include "newmat.h"
+#include "newimage/newimageall.h"
+
+using namespace Xfibres;
+
+
+void join_Parts(NEWIMAGE::volume<float> mask, string name_in, string name_out, string subjdir, int nvox, int nsamples, int nParts, float max, float min){
+ int size_parts = nvox/nParts;
+ int last_part = nvox - ((nParts-1)*size_parts);
+
+ //if(mean) nsamples=1;
+
+ Matrix result(nsamples,0);
+ Matrix part;
+
+ for(int i=0;i<(nParts-1);i++){
+ part.ReSize(nsamples,size_parts);
+ std::ostringstream num;
+ num << i;
+ std::string part_number;
+ part_number.assign(num.str());
+ std::string aux;
+ while(part_number.size()<4){
+ aux = "0" + part_number;
+ part_number.assign(aux);
+ }
+ std::string file_name;
+ file_name.assign(subjdir);
+ file_name += ".bedpostX/diff_parts/data_part_";
+ file_name += part_number;
+ file_name += "/";
+ file_name += name_in;
+ file_name += "J";
+
+ ifstream in;
+ in.open (file_name.data(), ios::in | ios::binary);
+ in.read((char*)&part(1,1), size_parts*nsamples*sizeof(Real));
+ in.close();
+
+ result = result | part;
+ }
+ part.ReSize(nsamples,last_part);
+ std::ostringstream num;
+ num << nParts-1;;
+ std::string part_number;
+ part_number.assign(num.str());
+ std::string aux;
+ while(part_number.size()<4){
+ aux = "0" + part_number;
+ part_number.assign(aux);
+ }
+ std::string file_name;
+ file_name.assign(subjdir);
+ file_name += ".bedpostX/diff_parts/data_part_";
+ file_name += part_number;
+ file_name += "/";
+ file_name += name_in;
+ file_name += "J";
+
+ ifstream in;
+ in.open (file_name.data(), ios::in | ios::binary);
+ in.read((char*)&part(1,1), last_part*nsamples*sizeof(Real));
+ in.close();
+ result = result | part;
+
+ NEWIMAGE::volume4D<float> tmp;
+ tmp.setmatrix(result,mask);
+ if(max==-10) max=tmp.max();
+ if(min==-10) min=tmp.min();
+ tmp.setDisplayMaximumMinimum(max,min);
+ save_volume4D(tmp,subjdir+".bedpostX/"+name_out);
+}
+
+//////////////////////////////////////////////////////////
+// MERGE THE OUTPUTS FILES OF BEDPOSTX
+//////////////////////////////////////////////////////////
+//parameters:
+// argc - 3 nvox
+// argc - 2 nParts
+// argc - 1 subjdir
+
+int main(int argc, char *argv[])
+{
+ // Setup logging:
+ Log& logger = LogSingleton::getInstance();
+ xfibresOptions& opts = xfibresOptions::getInstance();
+ opts.parse_command_line(argc-3,argv,logger);
+
+ NEWIMAGE::volume<float> mask;
+ read_volume(mask,opts.maskfile.value());
+
+ cout << opts.maskfile.value() << endl;
+
+ int nvox = atoi(argv[argc-3]);
+ int nParts = atoi(argv[argc-2]);
+ string subjdir = argv[argc-1];
+
+ int nsamples = opts.njumps.value()/opts.sampleevery.value();
+
+ //////////////////////////////////////////////////////////////
+ ////////// JOIN Results of the Parts //////////////////////
+ //////////////////////////////////////////////////////////////
+
+ if(opts.modelnum.value()==1){
+ join_Parts(mask,"mean_dsamples","mean_dsamples",subjdir, nvox, 1, nParts, -10, 0);
+ }else if(opts.modelnum.value()==2){
+ join_Parts(mask,"mean_dsamples","mean_dsamples",subjdir, nvox, 1, nParts, -10, 0);
+ join_Parts(mask,"mean_d_stdsamples","mean_d_stdsamples",subjdir, nvox, 1, nParts, -10, 0);
+ //join_Parts(mask,"dsamples","dsamples",subjdir, nvox, nsamples, nParts, -10, 0);
+ //join_Parts(mask,"d_stdsamples","d_stdsamples",subjdir, nvox, nsamples, nParts, -10, 0);
+ }
+ if (opts.f0.value()){
+ join_Parts(mask,"mean_f0samples","mean_f0samples",subjdir, nvox, 1, nParts, 1, 0);
+ //join_Parts(mask,"f0samples","f0samples",subjdir, nvox, nsamples, nParts, 1, 0);
+ }
+ if (opts.rician.value()){
+ join_Parts(mask,"mean_tausamples","mean_tausamples",subjdir, nvox, 1, nParts, -10, 0);
+ }
+ join_Parts(mask,"mean_S0samples","mean_S0samples",subjdir, nvox, 1, nParts, -10, 0);
+
+ for(int f=0;f<opts.nfibres.value();f++){
+ join_Parts(mask,"th"+num2str(f+1)+"samples","merged_th"+num2str(f+1)+"samples",subjdir, nvox, nsamples, nParts, -10, -10);
+ join_Parts(mask,"ph"+num2str(f+1)+"samples","merged_ph"+num2str(f+1)+"samples",subjdir, nvox, nsamples, nParts, -10, -10);
+ join_Parts(mask,"f"+num2str(f+1)+"samples","merged_f"+num2str(f+1)+"samples",subjdir, nvox, nsamples, nParts, 1, 0);
+
+ //join_Parts(mask,"mean_f"+num2str(f+1)+"samples",subjdir, nvox, 1, nParts, 1, 0);
+ //join_Parts(mask,"dyads"+num2str(f+1),subjdir, nvox, nsamples, nParts, 1, -1);
+ }
+
+ return 0;
+}
+
--
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