nifi header read done
This commit is contained in:
John Cupitt
parent
6dc6b4f722
commit
7716fa957b
@ -516,6 +516,14 @@ PKG_CHECK_MODULES(WIN32_GET_COMMAND_LINE, glib-2.0 >= 2.40,
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]
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)
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# from 2.48 we have g_uint_checked_mul() etc.
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PKG_CHECK_MODULES(HAVE_CHECKED_MUL, glib-2.0 >= 2.48,
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[AC_DEFINE(HAVE_CHECKED_MUL,1,[define if your glib has checked multiply.])
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],
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[:
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]
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)
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# check for gtk-doc
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GTK_DOC_CHECK([1.14],[--flavour no-tmpl])
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@ -34,6 +34,7 @@
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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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#ifdef HAVE_CONFIG_H
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#include <config.h>
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@ -68,22 +69,291 @@ 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 int
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vips_foreign_load_nifti_is_a( const char *filename )
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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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int datatype;
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VipsBandFormat fmt;
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} DT2Vips;
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static DT2Vips vips_DT2Vips[] = {
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{ DT_UNSIGNED_CHAR, VIPS_FORMAT_UCHAR },
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{ DT_SIGNED_SHORT, VIPS_FORMAT_SHORT },
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{ DT_SIGNED_INT, VIPS_FORMAT_INT },
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{ DT_FLOAT, VIPS_FORMAT_FLOAT },
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{ DT_COMPLEX, VIPS_FORMAT_COMPLEX },
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{ DT_DOUBLE, VIPS_FORMAT_DOUBLE },
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{ DT_RGB, VIPS_FORMAT_UCHAR }
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};
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/* Slow and horrid version if there's no recent glib.
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*/
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#ifndef HAVE_CHECKED_MUL
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#define g_uint_checked_mul( dest, a, b ) ( \
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((guint64) a * b) > UINT_MAX ? \
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(*dest = UINT_MAX, FALSE) : \
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(*dest = a * b, TRUE) \
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)
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#endif /*HAVE_CHECKED_MUL*/
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/* All the header fields we attach as metadata.
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*/
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typedef struct _Field {
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char *name;
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GType type;
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glong offset;
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} Field;
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static Field other_fields[] = {
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{ "ndim", G_TYPE_INT, G_STRUCT_OFFSET( nifti_image, ndim ) },
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{ "nx", G_TYPE_INT, G_STRUCT_OFFSET( nifti_image, nx ) },
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{ "ny", G_TYPE_INT, G_STRUCT_OFFSET( nifti_image, ny ) },
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{ "nz", G_TYPE_INT, G_STRUCT_OFFSET( nifti_image, nz ) },
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{ "nt", G_TYPE_INT, G_STRUCT_OFFSET( nifti_image, nt ) },
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{ "nu", G_TYPE_INT, G_STRUCT_OFFSET( nifti_image, nu ) },
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{ "nv", G_TYPE_INT, G_STRUCT_OFFSET( nifti_image, nv ) },
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{ "nw", G_TYPE_INT, G_STRUCT_OFFSET( nifti_image, nw ) },
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{ "dx", G_TYPE_FLOAT, G_STRUCT_OFFSET( nifti_image, dx ) },
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{ "dy", G_TYPE_FLOAT, G_STRUCT_OFFSET( nifti_image, dy ) },
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{ "dz", G_TYPE_FLOAT, G_STRUCT_OFFSET( nifti_image, dz ) },
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{ "dt", G_TYPE_FLOAT, G_STRUCT_OFFSET( nifti_image, dt ) },
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{ "du", G_TYPE_FLOAT, G_STRUCT_OFFSET( nifti_image, du ) },
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{ "dv", G_TYPE_FLOAT, G_STRUCT_OFFSET( nifti_image, dv ) },
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{ "dw", G_TYPE_FLOAT, G_STRUCT_OFFSET( nifti_image, dw ) },
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{ "scl_slope", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, scl_slope ) },
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{ "scl_inter", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, scl_inter ) },
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{ "cal_min", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, cal_min ) },
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{ "cal_max", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, cal_max ) },
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{ "qform_code", G_TYPE_INT,
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G_STRUCT_OFFSET( nifti_image, qform_code ) },
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{ "sform_code", G_TYPE_INT,
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G_STRUCT_OFFSET( nifti_image, sform_code ) },
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{ "freq_dim", G_TYPE_INT,
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G_STRUCT_OFFSET( nifti_image, freq_dim ) },
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{ "phase_dim", G_TYPE_INT,
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G_STRUCT_OFFSET( nifti_image, phase_dim ) },
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{ "slice_dim", G_TYPE_INT,
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G_STRUCT_OFFSET( nifti_image, slice_dim ) },
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{ "slice_code", G_TYPE_INT,
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G_STRUCT_OFFSET( nifti_image, slice_code ) },
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{ "slice_start", G_TYPE_INT,
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G_STRUCT_OFFSET( nifti_image, slice_start ) },
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{ "slice_end", G_TYPE_INT,
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G_STRUCT_OFFSET( nifti_image, slice_end ) },
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{ "slice_duration", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, slice_duration ) },
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{ "quatern_b", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, quatern_b ) },
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{ "quatern_c", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, quatern_c ) },
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{ "quatern_d", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, quatern_d ) },
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{ "qoffset_x", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, qoffset_x ) },
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{ "qoffset_y", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, qoffset_y ) },
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{ "qoffset_z", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, qoffset_z ) },
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{ "qfac", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, qfac ) },
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{ "sto_xyz00", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, sto_xyz.m[0][0] ) },
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{ "sto_xyz01", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, sto_xyz.m[0][1] ) },
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{ "sto_xyz02", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, sto_xyz.m[0][2] ) },
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{ "sto_xyz03", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, sto_xyz.m[0][3] ) },
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{ "sto_xyz10", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, sto_xyz.m[1][0] ) },
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{ "sto_xyz11", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, sto_xyz.m[1][1] ) },
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{ "sto_xyz12", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, sto_xyz.m[1][2] ) },
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{ "sto_xyz13", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, sto_xyz.m[1][3] ) },
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{ "sto_xyz20", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, sto_xyz.m[2][0] ) },
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{ "sto_xyz21", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, sto_xyz.m[2][1] ) },
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{ "sto_xyz22", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, sto_xyz.m[2][2] ) },
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{ "sto_xyz23", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, sto_xyz.m[2][3] ) },
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{ "sto_xyz30", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, sto_xyz.m[3][0] ) },
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{ "sto_xyz31", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, sto_xyz.m[3][1] ) },
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{ "sto_xyz32", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, sto_xyz.m[3][2] ) },
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{ "sto_xyz33", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, sto_xyz.m[3][3] ) },
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{ "toffset", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, toffset ) },
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{ "xyz_units", G_TYPE_INT,
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G_STRUCT_OFFSET( nifti_image, xyz_units ) },
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{ "time_units", G_TYPE_INT,
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G_STRUCT_OFFSET( nifti_image, time_units ) },
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{ "nifti_type", G_TYPE_INT,
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G_STRUCT_OFFSET( nifti_image, nifti_type ) },
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{ "intent_code", G_TYPE_INT,
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G_STRUCT_OFFSET( nifti_image, intent_code ) },
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{ "intent_p1", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, intent_p1 ) },
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{ "intent_p2", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, intent_p2 ) },
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{ "intent_p3", G_TYPE_FLOAT,
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G_STRUCT_OFFSET( nifti_image, intent_p3 ) },
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};
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/* How I wish glib had something like this :( Just implement the ones we need
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* for Field above.
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*/
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static void
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vips_gvalue_read( GValue *value, void *p )
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{
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nifti_image *nim;
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switch( G_VALUE_TYPE( value ) ) {
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case G_TYPE_INT:
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g_value_set_int( value, *((int *) p) );
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break;
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gboolean result;
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case G_TYPE_FLOAT:
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g_value_set_float( value, *((float *) p) );
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break;
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VIPS_DEBUG_MSG( "nifti_is_a: testing \"%s\"\n", filename );
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default:
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g_warning( "vips_gvalue_read: unsupported GType %s",
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g_type_name( G_VALUE_TYPE( value ) ) );
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}
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}
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result = FALSE;
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if( (nim = nifti_image_read( filename, FALSE )) ) {
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nifti_image_free( nim );
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result = TRUE;
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static int
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vips_foreign_load_nifti_get_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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guint width;
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guint height;
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guint bands;
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VipsBandFormat fmt;
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int i;
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char txt[256];
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if( nim->ndim < 1 ||
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nim->ndim > 7 ) {
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vips_error( class->nickname,
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_( "%d-dimensional images not supported" ),
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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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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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return( result );
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/* Unfold higher dimensions vertically. bands is updated below for
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* DT_RGB. Be careful to avoid height going over 2^31.
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*/
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bands = 1;
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width = (guint) nim->nx;
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height = (guint) nim->ny;
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for( i = 3; i < 8; i++ )
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if( !g_uint_checked_mul( &height, height, nim->dim[i] ) ) {
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vips_error( class->nickname,
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"%s", _( "dimension overflow" ) );
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return( 0 );
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}
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if( height > INT_MAX ) {
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vips_error( class->nickname, "%s", _( "dimension overflow" ) );
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return( 0 );
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}
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/* Decode voxel format.
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*/
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fmt = VIPS_FORMAT_UCHAR;
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for( i = 0; i < VIPS_NUMBER( vips_DT2Vips ); i++ )
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if( nim->datatype == vips_DT2Vips[i].datatype ) {
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fmt = vips_DT2Vips[i].fmt;
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break;
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}
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if( i == VIPS_NUMBER( vips_DT2Vips ) ) {
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vips_error( class->nickname,
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_( "datatype %d not supported" ), nim->datatype );
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return( -1 );
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}
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if( nim->datatype == DT_RGB )
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bands = 3;
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if( nim->datatype == DT_RGBA32 )
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bands = 4;
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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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printf( "get_vips_properties: bands = %d\n", bands );
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printf( "get_vips_properties: fmt = %d\n", fmt );
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#endif /*DEBUG*/
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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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for( i = 0; i < VIPS_NUMBER( other_fields ); i++ ) {
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GValue value = { 0 };
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g_value_init( &value, other_fields[i].type );
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vips_gvalue_read( &value,
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(gpointer) nim + other_fields[i].offset );
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vips_snprintf( txt, 256, "nifti-%s", other_fields[i].name );
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vips_image_set( out, txt, &value );
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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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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_image_set_string( out, "nifti-descrip", txt );
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for( i = 0; i < nim->num_ext; i++ ) {
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nifti1_extension *ext = &nim->ext_list[i];
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char *data_copy;
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vips_snprintf( txt, 256, "nifti-ext-%d-%d", i, ext->ecode );
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if( !(data_copy = vips_malloc( NULL, ext->esize )) )
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return( -1 );
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memcpy( data_copy, ext->edata, ext->esize );
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vips_image_set_blob( out, txt,
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(VipsCallbackFn) vips_free, data_copy, ext->esize );
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}
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return( 0 );
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}
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static int
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@ -103,8 +373,10 @@ vips_foreign_load_nifti_header( VipsForeignLoad *load )
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return( 0 );
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}
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/* Set load->out.
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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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return( -1 );
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}
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nifti_image_free( nim );
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@ -113,7 +385,12 @@ vips_foreign_load_nifti_header( VipsForeignLoad *load )
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return( 0 );
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}
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const char *vips__nifti_suffs[] = { ".nii", ".nii.gz", NULL };
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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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".img", ".img.gz",
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".nia", ".nia.gz",
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NULL };
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static void
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vips_foreign_load_nifti_class_init( VipsForeignLoadNiftiClass *class )
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@ -127,7 +404,7 @@ vips_foreign_load_nifti_class_init( VipsForeignLoadNiftiClass *class )
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gobject_class->get_property = vips_object_get_property;
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object_class->nickname = "niftiload";
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object_class->description = _( "load a FITS image" );
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object_class->description = _( "load a NIFTI image" );
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/* is_a() is not that quick ... lower the priority.
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*/
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@ -135,7 +412,7 @@ vips_foreign_load_nifti_class_init( VipsForeignLoadNiftiClass *class )
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foreign_class->suffs = vips__nifti_suffs;
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load_class->is_a = vips_foreign_load_nifti_is_a;
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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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VIPS_ARG_STRING( class, "filename", 1,
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