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changeset 1537:8b9213171e74

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Apply Peter Neelin patch for xfm concatenation. More test cases.
author stever <stever>
date Mon, 02 Jun 2003 02:49:35 +0000
parents 8acab48ddfff
children 83c26a940d5d
files .cvsignore BUGS ChangeLog Makefile.am TODO testdir/Makefile.am testdir/create_grid_xfm.c testdir/t1.xfm testdir/test_xfm.c testdir/xfmconcat_02.sh volume_io/MNI_formats/gen_xf_io.c volume_io/Testing/check_xfm.sh
diffstat 12 files changed, 197 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/.cvsignore
+++ b/.cvsignore
@@ -6,3 +6,4 @@
 Makefile.in
 aclocal.m4
 autom4te.cache
+configure
new file mode 100644
--- /dev/null
+++ b/BUGS
@@ -0,0 +1,12 @@
+Date: Tue, 06 May 2003 09:46:32 -0400
+From: Natasa Kovacevic <nkovacev@pandora.bioinfo.sickkids.on.ca>
+
+I beleive that there is a bug in xfmconcat in case when more then one
+grid transform gets concatenated (here I am refering to minc-1.0, so
+disregard the whole thing if it has been fixed in 1.1).  What happens
+is that all grid files involved in concatenation get the same
+name. This way they get overwritten during copying and the end product
+is a transfrom in which all displacement volumes are one and the same,
+namely the last one that appears in the concatenation.
+
+
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,9 +1,21 @@
 2003-06-01  Steve M. Robbins  <steve@nyongwa.montreal.qc.ca>
 
+	* testdir/Makefile.am (script_tests): 
+
+	* Makefile.am (SUBDIRS): Process volume_io before testdir,
+	because tests may link against volume_io.
+
+	* volume_io/MNI_formats/gen_xf_io.c (output_one_transform): 
+	Update *volume_count after writing a grid transform (thanks, Peter
+	Neelin).
+
 	* testdir/create_grid_xfm.c: New.  Utility to create grid
 	transformation.
 
-	* testdir/xfmconcat_01.sh: New.  Test concatenation of grid
+	* testdir/test_xfm.c: Copied from volume_io/Testing/test-xfm.c.
+
+	* testdir/xfmconcat_01.sh:
+	* testdir/xfmconcat_02.sh: New.  Test concatenation of grid
 	transformations.
 
 2003-03-17  Bert Vincent      <bert@bic.mni.mcgill.ca>
@@ -41,7 +53,7 @@
 2003-01-10  Steve M. Robbins  <steve@nyongwa.montreal.qc.ca>
 
 	* testdir/Makefile.am (INCLUDES): 
-	* volume_io/Testing//Makefile.am (INCLUDES): Set includes for
+	* volume_io/Testing/Makefile.am (INCLUDES): Set includes for
 	test files.
 
 	* Makefile.am (EXTRA_DIST, dist-hook): Distribute fortran
@@ -59,7 +71,7 @@
 	* volume_io/Documentation/Makefile.am: New.
 	
 	* volume_io/Testing/check_xfm.sh: 
-	* volume_io/Testing/check_xfm.sh
+	* volume_io/Testing/test-xfm.c:
 	* volume_io/Testing/t1.xfm:
 	* volume_io/Testing/t2.xfm:
 	* volume_io/Testing/t3.xfm:
--- a/Makefile.am
+++ b/Makefile.am
@@ -3,7 +3,7 @@
 AUTOMAKE_OPTIONS = check-news subdir-objects
 ACLOCAL_AMFLAGS = -I m4
 
-SUBDIRS = . testdir doc volume_io
+SUBDIRS = . volume_io testdir doc
 
 
 # Add these to the include searches.
--- a/TODO
+++ b/TODO
@@ -2,3 +2,10 @@
 
 * Add "-version" flag to all executables.
 
+* rationalize the testing into "testdir/".  I initially put 
+  stuff in volume_io/Testing in order to separate the testing of
+  minc proper from testing of volume_io.  But some of the "minc"
+  utilities (xfmconcat, xfminvert) use volume_io, so there is no
+  real separation, it seems.  Might as well move all testing stuff
+  to testdir.
+
--- a/testdir/Makefile.am
+++ b/testdir/Makefile.am
@@ -1,17 +1,21 @@
 INCLUDES = -I$(top_srcdir)/libsrc
-LDADD = ../libminc.la
+LDADD = ../libvolume_io.la ../libminc.la
 
-sh_tests = xfmconcat_01.sh
+script_tests = \
+	run_tests.csh \
+	xfmconcat_01.sh \
+	xfmconcat_02.sh
+
 all-local:
-	chmod +x $(sh_tests)
+	cd $(srcdir) && chmod +x $(script_tests)
 
-TESTS = run_tests.csh $(sh_tests)
+TESTS = $(script_tests)
 
 check_PROGRAMS = minc test_mconv minc_types icv icv_range \
 	icv_dim test_speed icv_dim1 icv_fillvalue \
-	create_grid_xfm
+	test_xfm create_grid_xfm
 
-EXTRA_DIST = run_tests.csh $(expect_files)
+EXTRA_DIST = $(script_tests) $(expect_files) t1.xfm
 
 CLEANFILES = test.mnc _*
 
@@ -34,5 +38,3 @@
 icv_range.out: ;
 minc_types.out: ;
 
-create_grid_xfm_LDADD = ../libvolume_io.la ../libminc.la
-
--- a/testdir/create_grid_xfm.c
+++ b/testdir/create_grid_xfm.c
@@ -3,7 +3,7 @@
 
 #include <stdio.h>
 #include <volume_io.h>
-#include "libsrc/time_stamp.h"
+#include "time_stamp.h"
 
 
 int main( int ac, char* av[] )
new file mode 100644
--- /dev/null
+++ b/testdir/t1.xfm
@@ -0,0 +1,8 @@
+MNI Transform File
+% Single linear transformation.
+
+Transform_Type = Linear;
+Linear_Transform =
+ 1 0 0 10
+ 0 1 0 20
+ 0 0 1 30;
new file mode 100644
--- /dev/null
+++ b/testdir/test_xfm.c
@@ -0,0 +1,91 @@
+
+#include <stdio.h>
+#include <stdlib.h>
+
+#include <volume_io.h>
+
+
+Real tolerance = 1e-8;
+
+
+int is_equal_real( Real e, Real a )
+{
+    return fabs(e-a) < tolerance;
+}
+
+
+
+/* Args: expected, actual.
+ */
+void assert_equal_point( Real ex, Real ey, Real ez,
+			 Real ax, Real ay, Real az,
+			 const char* msg )
+{
+    if ( is_equal_real(ex,ax) && 
+	 is_equal_real(ey,ay) &&
+	 is_equal_real(ez,az) )
+	return;
+
+    printf( "%s failure.\n"
+	    "Expected: %f %f %f\n"
+	    "  Actual: %f %f %f\n", 
+	    msg, ex,ey,ez,  ax,ay,az );
+
+    exit(3);
+}
+
+
+
+int main( int ac, char* av[] )
+{
+    int N;
+    General_transform xfm;
+
+
+    if ( ac != 3 && ac != 4 ) {
+	fprintf( stderr, "usage: %s N transform.xfm [tolerance]\n", av[0] );
+	return 1;
+    }
+
+    N = atoi( av[1] );
+    if ( input_transform_file( av[2], &xfm ) != OK ) {
+	fprintf( stderr, "Failed to load transform '%s'\n", av[2] );
+	return 2;
+    }
+
+    if ( ac == 4 ) {
+	tolerance = atof( av[3] );
+	printf( "Setting tolerance to %f.\n", tolerance );
+    }
+
+    while (N-- > 0) {
+	Real x = 500.0 * ( drand48() - 0.5 );
+	Real y = 500.0 * ( drand48() - 0.5 );
+	Real z = 500.0 * ( drand48() - 0.5 );
+
+	Real tx,ty,tz;
+	Real a,b,c;
+
+	general_transform_point( &xfm,  x,y,z,  &tx,&ty,&tz );
+
+	/* Check that general_inverse_transform_point() and
+	   invert_general_transform() behave sensibly.
+	*/
+	general_inverse_transform_point( &xfm,  tx,ty,tz,  &a,&b,&c );
+	assert_equal_point( x,y,z, a,b,c,
+			    "general_inverse_transform_point()" );
+
+	invert_general_transform( &xfm );
+
+	general_transform_point( &xfm, tx,ty,tz,  &a,&b,&c );
+	assert_equal_point( x,y,z, a,b,c,
+			    "general_transform_point() / inverted xfm" );
+
+	general_inverse_transform_point( &xfm,  x,y,z,  &a,&b,&c );
+	assert_equal_point( tx,ty,tz, a,b,c,
+			    "general_inverse_transform_point() / inverted xfm" );
+    }
+
+    return 0;
+}
+
new file mode 100755
--- /dev/null
+++ b/testdir/xfmconcat_02.sh
@@ -0,0 +1,42 @@
+#! /bin/sh
+#
+# Test application of concatenated transforms.
+
+set -e
+
+# _t1.xfm is linear transform.
+# _t2.xfm is inverse of _t1
+# _t3.xfm is grid transform.
+# _t4.xfm is inverse of _t3
+
+cp $srcdir/t1.xfm _t1.xfm
+../xfminvert _t1.xfm _t2.xfm
+dd if=/dev/zero | ../rawtominc -vector 3 -byte -clobber _grid.mnc 8 8 8
+./create_grid_xfm _grid.mnc _t3.xfm
+../xfminvert _t3.xfm _t4.xfm
+
+
+# Test primary transforms.
+#
+./test_xfm 10000 _t1.xfm
+./test_xfm 10000 _t2.xfm
+./test_xfm 10000 _t3.xfm
+./test_xfm 10000 _t4.xfm
+
+
+# Test concatenations.
+#
+../xfmconcat _t1.xfm _t3.xfm _t5.xfm
+./test_xfm 10000 _t5.xfm
+
+../xfmconcat _t1.xfm _t4.xfm _t6.xfm
+./test_xfm 10000 _t6.xfm
+
+../xfmconcat _t5.xfm _t6.xfm _t7.xfm
+./test_xfm 10000 _t7.xfm
+
+../xfminvert _t7.xfm _t8.xfm
+./test_xfm 10000 _t8.xfm
+
+../xfmconcat _t8.xfm _t2.xfm _t4.xfm _t7.xfm _t9.xfm
+./test_xfm 10000 _t9.xfm
--- a/volume_io/MNI_formats/gen_xf_io.c
+++ b/volume_io/MNI_formats/gen_xf_io.c
@@ -15,7 +15,7 @@
 #include  <internal_volume_io.h>
 
 #ifndef lint
-static char rcsid[] = "$Header: /private-cvsroot/minc/volume_io/MNI_formats/gen_xf_io.c,v 1.21 2001-04-24 13:38:47 neelin Exp $";
+static char rcsid[] = "$Header: /private-cvsroot/minc/volume_io/MNI_formats/gen_xf_io.c,v 1.22 2003-06-02 02:49:36 stever Exp $";
 #endif
 
 /*--------------------- file format keywords ------------------------------ */
@@ -64,6 +64,7 @@
 @OUTPUT     : 
 @RETURNS    : 
 @DESCRIPTION: Outputs a transform to the MNI transform file.
+            : Increment *volume_count.
 @METHOD     : 
 @GLOBALS    : 
 @CALLS      : 
@@ -180,6 +181,11 @@
         (void) sprintf( volume_filename, "%s_grid_%d.mnc", prefix_filename,
                         *volume_count );
 
+	/* Increment the volume counter as a side-effect to ensure that grid
+	 * files have different names.
+	 */
+	(*volume_count)++;
+
         /*--- decide where to write the volume file */
 
         base_filename = remove_directories_from_filename( volume_filename );
--- a/volume_io/Testing/check_xfm.sh
+++ b/volume_io/Testing/check_xfm.sh
@@ -6,8 +6,8 @@
 ./test-xfm 10000 $srcdir/t1.xfm
 ./test-xfm 10000 $srcdir/t2.xfm
 
-# Here's an illustration of how lousy the grid-transform inversion is:
-# using a tolerance of 0.8 will fail!
+# Transformation t3 is non-injective, so we have to set the tolerance
+# fairly large.
 ./test-xfm 10000 $srcdir/t3.xfm 0.9