Some qform/sform consistency stuff for the 3.3 release

fslorient.cc

@@ -17,16 +17,30 @@ void print_usage() {
   cout << "Usage: " << progname << " <main option> <filename>" << endl;
   cout << endl;
   cout << "  where the main option is one of:" << endl;
-  cout << "    -forceradiological     (makes radiological header)" << endl;
-  cout << "    -forceneurological     (makes neurological header - not Analyze)" << endl;
-  cout << "    -swaporient            (swaps radiological and neurological)" << endl;
-  cout << "    -getorient             (prints left-right orientation)" << endl;
-  cout << "    -deleteorient          (removes orient info from header - not Analyze)" << endl;
+  cout << "    -getorient             (prints FSL left-right orientation)" << endl;
+  cout << "    -getsform              (prints the 16 elements of the sform matrix)" << endl;
+  cout << "    -getqform              (prints the 16 elements of the qform matrix)" << endl;
+  cout << "    -setsform <m11 m12 ... m44>  (sets the 16 elements of the sform matrix)" << endl;
+  cout << "    -setqform <m11 m12 ... m44>  (sets the 16 elements of the qform matrix)" << endl;
+  cout << "    -getsformcode          (prints the sform integer code)" << endl;
+  cout << "    -getqformcode          (prints the qform integer code)" << endl;
+  cout << "    -setsformcode <code>   (sets sform integer code)" << endl;
+  cout << "    -setqformcode <code>   (sets qform integer code)" << endl;
+  cout << "    -copysform2qform       (sets the qform equal to the sform - code and matrix)" << endl;
+  cout << "    -copyqform2sform       (sets the sform equal to the qform - code and matrix)" << endl;
+  cout << "    -deleteorient          (removes orient info from header)" << endl;
+  cout << "    -forceradiological     (makes FSL radiological header)" << endl;
+  cout << "    -forceneurological     (makes FSL neurological header - not Analyze)" << endl;
+  cout << "    -swaporient            (swaps FSL radiological and FSL neurological)" << endl;
   cout << endl;
-  cout << " Note: The stored data order is never changed here - only the header info." << endl;
+  cout << " Note: ANALYZE files are NOT modified by any of the commands" << endl;
+  cout << "         - they are for NIFTI files ONLY!" << endl;
+  cout << "       For NIFTI: the stored data order is never changed here - only the header info." << endl;
   cout << "       To change the data storage use avwswapdim." << endl;
   cout << endl;
   cout << "  e.g.  " << progname << " -forceradiological myimage" << endl;
+  cout << "        " << progname << " -copysform2qform myimage" << endl;
+  cout << "        " << progname << " -setsform -2 0 0 90 0 2 0 -126 0 0 2 -72 0 0 0 1 myimage" << endl;
   cout << endl;
 }
 
@@ -42,51 +56,144 @@ void swaporient(volume4D<T>& invol) {
   invol.set_qform(invol.qform_code(),invol.qform_mat() * swapmat);
 }
 
+
+template <class T>
+int getorient(const volume4D<T>& invol) 
+{
+  if (invol.left_right_order()==FSL_RADIOLOGICAL) { 
+    cout << "RADIOLOGICAL" << endl;
+  } else {
+    cout << "NEUROLOGICAL" << endl;
+  }
+  return 0;
+}
+
+
+template <class T>
+int getorient(const string& filename) 
+{
+  volume4D<T> invol;
+  read_volume4D(invol,filename);
+  return getorient(invol);
+}
+
+
+int showmat(const Matrix& mat) {
+  for (int a=1; a<=4; a++) {
+    for (int b=1; b<=4; b++) {
+      cout << mat(a,b) << " ";
+    }
+  }
+  cout << endl;
+  return 0;
+}
+
+
+int testminargs(int argnum, int argc) {
+  if (argc < (argnum + 1)) {
+    print_usage();
+    exit(EXIT_FAILURE);
+  }
+  return 0;
+}
+
+
 template <class T>
 int fmrib_main(int argc,char *argv[])
 {
+  bool modified=false;
   int retval=0;
-  string option=argv[1], filename=argv[2];
+  string option=argv[1], filename;
 
   volumeinfo volinfo;
   volume4D<T> invol;
+
+  filename=argv[argc-1];
   read_volume4D(invol,filename,volinfo);
 
-  if (option=="-forceradiological") {
+  if (option=="-getorient") {
+    getorient(invol);
+  } else if (option=="-getsformcode") {
+    cout << invol.sform_code() << endl;
+  } else if (option=="-getqformcode") {
+    cout << invol.qform_code() << endl;
+  } else if (option=="-getqform") {
+    showmat(invol.qform_mat());
+  } else if (option=="-getsform") {
+    showmat(invol.sform_mat());
+  } else if (option=="-setsformcode") {
+    testminargs(3,argc);
+    modified=true;
+    int code = (int) atof(argv[2]);
+    invol.set_sform(code,invol.sform_mat());
+  } else if (option=="-setqformcode") {
+    testminargs(3,argc);
+    modified=true;
+    int code = (int) atof(argv[2]);
+    invol.set_qform(code,invol.qform_mat());
+  } else if ( (option=="-setqform") || (option=="-setsform") ) {
+    testminargs(18,argc);
+    modified=true;
+    Matrix mat(4,4);
+    for (int a=1; a<=4; a++) {
+      for (int b=1; b<=4; b++) {
+	mat(a,b)=atof(argv[a*4+b-3]);
+      }
+    }
+    // override the last line
+    mat(4,1)=0; mat(4,2)=0; mat(4,3)=0; mat(4,4)=1;
+    if (option=="-setqform") {
+      invol.set_qform(invol.qform_code(),mat);
+    }
+    if (option=="-setsform") {
+      invol.set_sform(invol.sform_code(),mat);
+    }
+  } else if (option=="-copysform2qform") {
+    modified=true;
+    invol.set_qform(invol.sform_code(),invol.sform_mat());
+  } else if (option=="-copyqform2sform") {
+    modified=true;
+    invol.set_sform(invol.qform_code(),invol.qform_mat());
+  } else if (option=="-swaporient") {
+    modified=true;
+    swaporient(invol);
+  } else if (option=="-deleteorient") {
+    modified=true;
+    invol.set_sform(NIFTI_XFORM_UNKNOWN,invol.sform_mat());
+    invol.set_qform(NIFTI_XFORM_UNKNOWN,invol.qform_mat());
+  } else if (option=="-forceradiological") {
+    modified=true;
     if (invol.left_right_order()==FSL_NEUROLOGICAL) {
       swaporient(invol);
     }
   } else if (option=="-forceneurological") {
+    modified=true;
     if (invol.left_right_order()==FSL_RADIOLOGICAL) {
       swaporient(invol);
     }
-  } else if (option=="-swaporient") {
-    swaporient(invol);
-  } else if (option=="-getorient") {
-    if (invol.left_right_order()==FSL_RADIOLOGICAL) { 
-      cout << "RADIOLOGICAL" << endl;
+  } else{
+    // does the first arg exist as an image file?
+    if (fsl_imageexists(string(argv[1]))) {
+      getorient<T>(string(argv[1]));
     } else {
-      cout << "NEUROLOGICAL" << endl;
+      cerr << "Unrecognised option: " << option << endl;
+      print_usage();
+      retval = -1;
     }
-    return 0;
-  } else if (option=="-deleteorient") {
-    invol.set_sform(NIFTI_XFORM_UNKNOWN,invol.sform_mat());
-    invol.set_qform(NIFTI_XFORM_UNKNOWN,invol.qform_mat());
-  } else{
-    cerr << "Unrecognised option: " << option << endl;
-    print_usage();
-    retval = -1;
   }
 
-  if (FslBaseFileType(FslGetFileType(&volinfo))!=FSL_TYPE_ANALYZE) {
-    FslSetOverrideOutputType(FslGetFileType(&volinfo));
-    write_volume4D(invol,filename,volinfo);
-    FslSetOverrideOutputType(-1);  // restore to default
-  } else {
-    cerr << "Cannot modify orientation for Analyze files" << endl;
-    cerr << "  All Analyze files are treated as radiological" << endl;
-    cerr << "  To change the data storage use avwswapdim" << endl;
-    retval=-1;
+
+  if (modified) {
+    if (FslBaseFileType(FslGetFileType(&volinfo))!=FSL_TYPE_ANALYZE) {
+      FslSetOverrideOutputType(FslGetFileType(&volinfo));
+      write_volume4D(invol,filename,volinfo);
+      FslSetOverrideOutputType(-1);  // restore to default
+    } else {
+      cerr << "Cannot modify orientation for Analyze files" << endl;
+      cerr << "  All Analyze files are treated as radiological" << endl;
+      cerr << "  To change the data storage use avwswapdim" << endl;
+      retval=-1;
+    }
   }
   return retval;
 }
@@ -94,12 +201,13 @@ int fmrib_main(int argc,char *argv[])
   
 int main(int argc,char *argv[])
 {
-  if (argc<3) { 
+  if (argc<2) { 
     print_usage();
     return -1; 
   }
   
-  string inname = argv[2];
+  string inname;
+  inname = argv[argc-1];
   // call the templated main
   return call_fmrib_main(dtype(inname),argc,argv);
 }