load seems to work
This commit is contained in:
John Cupitt
parent
7716fa957b
commit
06e8d1d523
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@ -1,7 +1,7 @@
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/* load nifti from a file
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*
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* 29/6/18
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* - from niftiload.c
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* - from fitsload.c
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*/
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/*
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@ -33,8 +33,13 @@
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/*
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#define DEBUG
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*/
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#define VIPS_DEBUG
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*/
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/* TODO
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* - for uncompressed images, we could offer direct mapping of the input
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* - could stream the image perhaps?
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*/
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#ifdef HAVE_CONFIG_H
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#include <config.h>
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@ -62,6 +67,8 @@ typedef struct _VipsForeignLoadNifti {
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*/
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char *filename;
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nifti_image *nim;
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} VipsForeignLoadNifti;
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typedef VipsForeignLoadClass VipsForeignLoadNiftiClass;
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@ -69,6 +76,17 @@ typedef VipsForeignLoadClass VipsForeignLoadNiftiClass;
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G_DEFINE_TYPE( VipsForeignLoadNifti, vips_foreign_load_nifti,
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VIPS_TYPE_FOREIGN_LOAD );
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static void
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vips_foreign_load_nifti_dispose( GObject *gobject )
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{
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VipsForeignLoadNifti *nifti = (VipsForeignLoadNifti *) gobject;
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VIPS_FREEF( nifti_image_free, nifti->nim );
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G_OBJECT_CLASS( vips_foreign_load_nifti_parent_class )->
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dispose( gobject );
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}
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/* Map DT_* datatype values to VipsBandFormat.
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*/
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typedef struct _DT2Vips {
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@ -246,7 +264,7 @@ vips_gvalue_read( GValue *value, void *p )
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}
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static int
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vips_foreign_load_nifti_get_header( VipsForeignLoadNifti *nifti,
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vips_foreign_load_nifti_set_header( VipsForeignLoadNifti *nifti,
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nifti_image *nim, VipsImage *out )
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{
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VipsObjectClass *class = VIPS_OBJECT_GET_CLASS( nifti );
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@ -255,6 +273,8 @@ vips_foreign_load_nifti_get_header( VipsForeignLoadNifti *nifti,
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guint height;
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guint bands;
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VipsBandFormat fmt;
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double xres;
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double yres;
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int i;
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char txt[256];
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@ -265,11 +285,23 @@ vips_foreign_load_nifti_get_header( VipsForeignLoadNifti *nifti,
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nim->ndim );
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return( 0 );
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}
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for( i = 1; i < 8; i++ )
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for( i = 1; i < 8; i++ ) {
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if( nim->dim[i] <= 0 ) {
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vips_error( class->nickname,
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"%s", _( "invalid dimension" ) );
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return( 0 );
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}
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/* If we have several images in a dimension, the spacing must
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* be non-zero, or we'll get a /0 error in resolution
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* calculation.
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*/
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if( nim->dim[i] > 1 &&
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nim->pixdim[i] == 0 ) {
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vips_error( class->nickname,
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"%s", _( "invalid resolution" ) );
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return( 0 );
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}
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}
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/* Unfold higher dimensions vertically. bands is updated below for
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@ -308,6 +340,31 @@ vips_foreign_load_nifti_get_header( VipsForeignLoadNifti *nifti,
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if( nim->datatype == DT_RGBA32 )
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bands = 4;
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/* We fold y and z together, so they must have the same resolution..
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*/
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xres = 1.0;
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yres = 1.0;
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if( nim->nz == 1 ||
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nim->dz == nim->dy )
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switch( nim->xyz_units ) {
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case NIFTI_UNITS_METER:
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xres = 1000.0 / nim->dx;
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yres = 1000.0 / nim->dy;
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break;
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case NIFTI_UNITS_MM:
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xres = 1.0 / nim->dx;
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yres = 1.0 / nim->dy;
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break;
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case NIFTI_UNITS_MICRON:
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xres = 1.0 / (1000.0 * nim->dx);
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yres = 1.0 / (1000.0 * nim->dy);
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break;
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default:
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break;
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}
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#ifdef DEBUG
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printf( "get_vips_properties: width = %d\n", width );
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printf( "get_vips_properties: height = %d\n", height );
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@ -315,12 +372,13 @@ vips_foreign_load_nifti_get_header( VipsForeignLoadNifti *nifti,
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printf( "get_vips_properties: fmt = %d\n", fmt );
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#endif /*DEBUG*/
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vips_image_pipelinev( out, VIPS_DEMAND_STYLE_SMALLTILE, NULL );
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vips_image_init_fields( out,
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width, height, bands, fmt,
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VIPS_CODING_NONE,
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bands == 1 ?
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VIPS_INTERPRETATION_B_W : VIPS_INTERPRETATION_sRGB,
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1.0, 1.0 );
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xres, yres );
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for( i = 0; i < VIPS_NUMBER( other_fields ); i++ ) {
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GValue value = { 0 };
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@ -333,12 +391,12 @@ vips_foreign_load_nifti_get_header( VipsForeignLoadNifti *nifti,
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g_value_unset( &value );
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}
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vips_strncpy( txt, nim->intent_name, 16 );
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txt[16] = '\0';
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/* One byte longer than the spec to leave space for any extra
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* '\0' termination.
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*/
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vips_strncpy( txt, nim->intent_name, 17 );
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vips_image_set_string( out, "nifti-intent_name", txt );
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vips_strncpy( txt, nim->descrip, 80 );
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txt[80] = '\0';
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vips_strncpy( txt, nim->descrip, 81 );
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vips_image_set_string( out, "nifti-descrip", txt );
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for( i = 0; i < nim->num_ext; i++ ) {
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@ -362,29 +420,86 @@ vips_foreign_load_nifti_header( VipsForeignLoad *load )
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VipsObjectClass *class = VIPS_OBJECT_GET_CLASS( load );
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VipsForeignLoadNifti *nifti = (VipsForeignLoadNifti *) load;
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nifti_image *nim;
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/* We can't use the (much faster) nifti_read_header() since it just
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* reads the 348 bytes iof the analyze struct and does not read any of
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* the extension fields.
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*/
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/* FALSE means don't read data, just the header. Use
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* nifti_image_load() later to pull the data in.
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*/
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if( !(nim = nifti_image_read( nifti->filename, FALSE )) ) {
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if( !(nifti->nim = nifti_image_read( nifti->filename, FALSE )) ) {
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vips_error( class->nickname,
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"%s", _( "unable to read NIFTI file" ) );
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"%s", _( "unable to read NIFTI header" ) );
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return( 0 );
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}
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if( vips_foreign_load_nifti_get_header( nifti, nim, load->out ) ) {
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nifti_image_free( nim );
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if( vips_foreign_load_nifti_set_header( nifti,
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nifti->nim, load->out ) ) {
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return( -1 );
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}
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nifti_image_free( nim );
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VIPS_SETSTR( load->out->filename, nifti->filename );
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return( 0 );
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}
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static int
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vips_foreign_load_nifti_generate( VipsRegion *out,
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void *seq, void *a, void *b, gboolean *stop )
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{
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VipsForeignLoadNifti *nifti = (VipsForeignLoadNifti *) a;
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VipsRect *r = &out->valid;
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size_t len = VIPS_REGION_SIZEOF_LINE( out );
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size_t line_stride = VIPS_IMAGE_SIZEOF_LINE( out->im );
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size_t pixel_stride = VIPS_IMAGE_SIZEOF_PEL( out->im );
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int y;
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VIPS_DEBUG_MSG( "vips_foreign_load_nifti_generate: "
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"generating left = %d, top = %d, width = %d, height = %d\n",
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r->left, r->top, r->width, r->height );
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for( y = r->top; y < VIPS_RECT_BOTTOM( r ); y++ ) {
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VipsPel *q = VIPS_REGION_ADDR( out, r->left, y );
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VipsPel *p = (VipsPel *) nifti->nim->data +
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y * line_stride +
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r->left * pixel_stride;
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memcpy( q, p, len );
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}
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return( 0 );
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}
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static int
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vips_foreign_load_nifti_load( VipsForeignLoad *load )
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{
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VipsObjectClass *class = VIPS_OBJECT_GET_CLASS( load );
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VipsForeignLoadNifti *nifti = (VipsForeignLoadNifti *) load;
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#ifdef DEBUG
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printf( "vips_foreign_load_nifti_load: loading image\n" );
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#endif /*DEBUG*/
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if( nifti_image_load( nifti->nim ) ) {
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vips_error( class->nickname,
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"%s", _( "unable to load NIFTI file" ) );
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return( -1 );
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}
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if( vips_foreign_load_nifti_set_header( nifti,
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nifti->nim, load->real ) )
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return( -1 );
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if( vips_image_generate( load->real,
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NULL, vips_foreign_load_nifti_generate, NULL, nifti, NULL ) )
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return( -1 );
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return( 0 );
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}
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const char *vips__nifti_suffs[] = {
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".nii", ".nii.gz",
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".hdr", ".hdr.gz",
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@ -400,6 +515,7 @@ vips_foreign_load_nifti_class_init( VipsForeignLoadNiftiClass *class )
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VipsForeignClass *foreign_class = (VipsForeignClass *) class;
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VipsForeignLoadClass *load_class = (VipsForeignLoadClass *) class;
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gobject_class->dispose = vips_foreign_load_nifti_dispose;
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gobject_class->set_property = vips_object_set_property;
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gobject_class->get_property = vips_object_get_property;
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@ -414,6 +530,7 @@ vips_foreign_load_nifti_class_init( VipsForeignLoadNiftiClass *class )
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load_class->is_a = is_nifti_file;
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load_class->header = vips_foreign_load_nifti_header;
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load_class->load = vips_foreign_load_nifti_load;
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VIPS_ARG_STRING( class, "filename", 1,
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_( "Filename" ),
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