From 3019e26b6a71f34bbb4162a94e52a0fc3395f9b1 Mon Sep 17 00:00:00 2001
From: Saad Jbabdi <saad@fmrib.ox.ac.uk>
Date: Tue, 11 Dec 2007 16:07:59 +0000
Subject: [PATCH] added directory option
---
ccops.cc | 43 ++++++++++++++++++++++++-------------------
ccopsOptions.h | 9 +++++++--
2 files changed, 31 insertions(+), 21 deletions(-)
diff --git a/ccops.cc b/ccops.cc
index 24dd0d5..ce52a0c 100644
--- a/ccops.cc
+++ b/ccops.cc
@@ -395,6 +395,10 @@ int main ( int argc, char **argv ){
ccopsOptions& opts = ccopsOptions::getInstance();
int success=opts.parse_command_line(argc,argv);
if(!success) return 1;
+ if(opts.inmatrix.value()=="" && opts.directory.value()==""){
+ cerr << "Specify either input matrix or tractography directory" << endl;
+ return 1;
+ }
string ip=opts.inmatrix.value();
make_basename(ip);
@@ -403,8 +407,9 @@ int main ( int argc, char **argv ){
volume<int> coordvol;
volume<int> tractcoordvol;
bool coordbool=false,tractcoordbool=false;
- read_volume(myOM,ip);
-
+ // read_volume(myOM,ip);
+ read_volume(myOM,opts.directory.value()+"/"+opts.inmatrix.value());
+
Matrix myOMmat(myOM.xsize(),myOM.ysize());
Matrix mycoordmat,mytractcoordmat;
Matrix newOMmat,newcoordmat,newtractcoordmat;
@@ -426,7 +431,7 @@ int main ( int argc, char **argv ){
// write_ascii_matrix(newOMmat.t(),"preprecock");
//Checking for and loading up Seed Coordinates
- string coordname="coords_for_"+ip;
+ string coordname=opts.directory.value()+"/coords_for_"+ip;
if(fsl_imageexists(coordname)){
read_volume(coordvol,coordname);
coordbool=true;
@@ -442,7 +447,7 @@ int main ( int argc, char **argv ){
}
//Checking For and Loading Up Tract coordinates
- string trcoordname="tract_space_coords_for_"+ip;
+ string trcoordname=opts.directory.value()+"/tract_space_coords_for_"+ip;
if(fsl_imageexists(trcoordname)){
read_volume(tractcoordvol,trcoordname);
tractcoordbool=true;
@@ -467,7 +472,7 @@ int main ( int argc, char **argv ){
if(opts.excl_mask.value()!=""){
volume<int> lookup_tract;
volume<int> excl;
- read_volume(lookup_tract,"lookup_tractspace_"+ip);
+ read_volume(lookup_tract,opts.directory.value()+"/lookup_tractspace_"+ip);
string exname=opts.excl_mask.value();
make_basename(exname);
read_volume(excl,exname);
@@ -555,8 +560,8 @@ int main ( int argc, char **argv ){
}
}
- save_volume(outCCvol,"CC_"+base);
- save_volume(outcoords,"coords_for_"+base);
+ save_volume(outCCvol,opts.directory.value()+"/CC_"+base);
+ save_volume(outcoords,opts.directory.value()+"/coords_for_"+base);
}
else{
@@ -588,16 +593,16 @@ int main ( int argc, char **argv ){
}
}
- write_ascii_matrix(r1,base+"r1");
- write_ascii_matrix(y1,base+"y1");
- save_volume(outCCvol,"reord_CC_"+base);
- save_volume(outcoords,"coords_for_reord_"+base);
+ write_ascii_matrix(r1,opts.directory.value()+"/"+base+"r1");
+ write_ascii_matrix(y1,opts.directory.value()+"/"+base+"y1");
+ save_volume(outCCvol,opts.directory.value()+"/reord_CC_"+base);
+ save_volume(outcoords,opts.directory.value()+"/coords_for_reord_"+base);
// save clustering if kmeans used
if(opts.scheme.value() == "kmeans"){
volume<int> mask;
if(opts.mask.value() == "")
- read_volume(mask,"fdt_paths");
+ read_volume(mask,opts.directory.value()+"/fdt_paths");
else
read_volume(mask,opts.mask.value());
mask = 0;
@@ -606,11 +611,11 @@ int main ( int argc, char **argv ){
outcoords(i,1,0),
outcoords(i,2,0)) = (int)y1(i+1) + 1;
}
- save_volume(mask,"reord_mask_"+base);
+ save_volume(mask,opts.directory.value()+"/reord_mask_"+base);
// save tractspace clustering if specified
volume<int> outmask,tractmask;
- read_volume(tractmask,"lookup_tractspace_fdt_matrix2");
+ read_volume(tractmask,opts.directory.value()+"/lookup_tractspace_fdt_matrix2");
outmask=tractmask;
copybasicproperties(tractmask,outmask);
@@ -628,7 +633,7 @@ int main ( int argc, char **argv ){
vals.Maximum1(index);
outmask(x,y,z) = (int)y1(index);
}
- save_volume(outmask,"tract_clustering_"+base);
+ save_volume(outmask,opts.directory.value()+"/tract_clustering_"+base);
}
@@ -650,8 +655,8 @@ int main ( int argc, char **argv ){
return(-1);
}
- write_ascii_matrix(r2,base+"r2");
- write_ascii_matrix(y2,base+"y2");
+ write_ascii_matrix(r2,opts.directory.value()+"/"+base+"r2");
+ write_ascii_matrix(y2,opts.directory.value()+"/"+base+"y2");
volume<int> outvol(newOMmat.Nrows(),newOMmat.Ncols(),1);
volume<int> outtractcoords(newtractcoordmat.Nrows(),3,1);
@@ -672,8 +677,8 @@ int main ( int argc, char **argv ){
outtractcoords(i,2,0)=(int)newtractcoordmat(int(r2(i+1)),3);
}
}
- save_volume(outvol,"reord_"+base);
- save_volume(outtractcoords,"tract_space_coords_for_reord_"+base);
+ save_volume(outvol,opts.directory.value()+"/reord_"+base);
+ save_volume(outtractcoords,opts.directory.value()+"/tract_space_coords_for_reord_"+base);
}
return 0;
}
diff --git a/ccopsOptions.h b/ccopsOptions.h
index c0038b3..833efdc 100644
--- a/ccopsOptions.h
+++ b/ccopsOptions.h
@@ -27,6 +27,7 @@ class ccopsOptions {
Option<bool> help;
Option<string> inmatrix;
Option<string> basename;
+ Option<string> directory;
Option<string> excl_mask;
Option<bool> reord1;
Option<bool> reord2;
@@ -60,12 +61,15 @@ class ccopsOptions {
help(string("-h,--help"), false,
string("display this message"),
false, no_argument),
- inmatrix(string("-i,--in"), string(""),
+ inmatrix(string("-i,--in"), string("fdt_matrix2"),
string("input matrix"),
- true, requires_argument),
+ false, requires_argument),
basename(string("-b,--basename"), string(""),
string("Output basename"),
true, requires_argument),
+ directory(string("-d,--dir"), string(""),
+ string("Tractography Results Directory"),
+ false, requires_argument),
excl_mask(string("-x"), string(""),
string("exclusion mask (in tract space johannes)"),
false, requires_argument),
@@ -101,6 +105,7 @@ class ccopsOptions {
options.add(help);
options.add(inmatrix);
options.add(basename);
+ options.add(directory);
options.add(excl_mask);
options.add(reord1);
options.add(reord2);
--
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