Removed remaining dependencies to minc and added volume_io to 3rdparty

.gitignore

@@ -1,26 +1,21 @@
+.deps
+.dirstamp
+.libs
 autom4te.cache
 aclocal.m4
 config.*
-m4
-Progs/.deps
 Makefile.in
-Progs/Makefile.in
 compile
 configure
 install-sh
 ltmain.sh
 missing
 stamp-h1
-*/.deps
-*/.dirstamp
-Progs/.libs
 depcomp
 libtool
 Makefile
-.libs
 build*
 log*
-.deps
 configure~
 Progs/CAT_3dVol2Surf
 Progs/CAT_AddValuesToSurf

3rdparty/README.md

@@ -1,14 +1,12 @@
 This directory contains libraries that are not maintained by the CAT-Surface
-maintainers. These libraries are necessary to compile CAT_Surface and are 
-provided here as courtesy to the end-users.
+maintainers. These libraries are needed to compile CAT_Surface and are provided 
+here as a courtesy to end users.
 
-The following library was largely modified:
+The following libraries have undergone major changes and all dependencies on 
+volume functions have been removed, since we are constantly using nifti functions
+only:
 - [bicp-1.4.6](https://github.com/BIC-MNI/minc)
+- [minc-1.5.1/volume_io](https://github.com/BIC-MNI/minc)
 
-All dependencies in bicpl on minc and volume_io were removed and replaced by 
-nifti-functions. The following functions from minc were added:
+The following function was added from minc-1.5.1:
 - ParseArgv.c
-- alloc.c
-- alloc_check.c
-- progress.c
-- arrays.c

3rdparty/bicpl-surface/Include/bicpl.h

@@ -36,7 +36,6 @@ extern "C" {
 #include  <bicpl/numerical.h>
 #include  <bicpl/objects.h>
 #include  <bicpl/prog_utils.h>
-#include  <alloc.h>
 //#include  <bicpl/vols.h>
 //#include  <bicpl/images.h>
 

3rdparty/bicpl-surface/Objects/graphics_io.c

@@ -0,0 +1,119 @@
+/* ----------------------------------------------------------------------------
+@COPYRIGHT  :
+              Copyright 1993,1994,1995 David MacDonald,
+              McConnell Brain Imaging Centre,
+              Montreal Neurological Institute, McGill University.
+              Permission to use, copy, modify, and distribute this
+              software and its documentation for any purpose and without
+              fee is hereby granted, provided that the above copyright
+              notice appear in all copies.  The author and McGill University
+              make no representations about the suitability of this
+              software for any purpose.  It is provided "as is" without
+              express or implied warranty.
+---------------------------------------------------------------------------- */
+
+#include "bicpl_internal.h"
+
+#ifndef lint
+static char rcsid[] = "$Header: /private-cvsroot/libraries/bicpl/Objects/graphics_io.c,v 1.9 2005/08/17 22:28:26 bert Exp $";
+#endif
+
+/* ----------------------------- MNI Header -----------------------------------
+@NAME       : input_graphics_file
+@INPUT      : filename
+@OUTPUT     : format
+              n_objects
+              object_list
+@RETURNS    : OK or ERROR
+@DESCRIPTION: Inputs a file of graphics objects.
+@METHOD     : 
+@GLOBALS    : 
+@CALLS      : 
+@CREATED    :         1993    David MacDonald
+@MODIFIED   : 
+---------------------------------------------------------------------------- */
+
+BICAPI  Status   input_graphics_file(
+    STRING         filename,
+    File_formats   *format,
+    int            *n_objects,
+    object_struct  ***object_list )
+{
+    Status         status;
+    FILE           *file;
+    BOOLEAN        eof;
+    object_struct  *object;
+    STRING         current_directory;
+
+    status = open_file_with_default_suffix( filename, "obj", READ_FILE,
+                                            BINARY_FORMAT, &file );
+
+    *n_objects = 0;
+
+    if( status == OK )
+    {
+        current_directory = extract_directory( filename );
+
+        do
+        {
+            status = input_object( current_directory, file, format,
+                                   &object, &eof );
+
+            if( status == OK && !eof )
+                add_object_to_list( n_objects, object_list, object );
+
+        } while( status == OK && !eof );
+
+        delete_string( current_directory );
+    }
+
+    if( status == OK )
+        status = close_file( file );
+
+    return( status );
+}
+
+/* ----------------------------- MNI Header -----------------------------------
+@NAME       : output_graphics_file
+@INPUT      : filename
+              format
+              n_objects
+              object_list
+@OUTPUT     : 
+@RETURNS    : OK or ERROR
+@DESCRIPTION: Writes a file of graphics objects.
+@METHOD     : 
+@GLOBALS    : 
+@CALLS      : 
+@CREATED    :         1993    David MacDonald
+@MODIFIED   : 
+---------------------------------------------------------------------------- */
+
+BICAPI  Status   output_graphics_file(
+    STRING         filename,
+    File_formats   format,
+    int            n_objects,
+    object_struct  *object_list[] )
+{
+    Status         status;
+    int            i;
+    FILE           *file;
+
+    status = open_file_with_default_suffix( filename, "obj", WRITE_FILE,
+                                            BINARY_FORMAT, &file );
+
+    if( status == OK )
+    {
+        for_less( i, 0, n_objects )
+        {
+            if( status == OK )
+                status = output_object( file, format, object_list[i] );
+        }
+    }
+
+    if( status == OK )
+        status = close_file( file );
+
+    return( status );
+}
+