/* ----------------------------- MNI Header -----------------------------------
@NAME : handle_normalization
@INPUT : reshape_info - information for reshaping volume
block_start - start of current block
block_count - count for current block
minmax_buffer - buffer space for getting min and max
values
@OUTPUT : fillvalue - pixel fill value to use for this block
@RETURNS : (none)
@DESCRIPTION: Sets up icv for normalization to ensure that block is
internally normalized. Output image-max and min are set.
The appropriate pixel fill value is calculated for this
min and max (applies to the whole block).
@METHOD :
@GLOBALS :
@CALLS :
@CREATED : October 25, 1994 (Peter Neelin)
@MODIFIED :
---------------------------------------------------------------------------- */
static void handle_normalization(Reshape_info *reshape_info,
long *block_start,
long *block_count,
double *minmax_buffer,
double *fillvalue)
{
int iloop;
int inmincid, inimgid, varid, icvid;
long minmax_start[MAX_VAR_DIMS];
double minimum, maximum, *extreme, valid_min, valid_max, denom;
char *varname;
/* Get input minc id, image id and icv id*/
inmincid = reshape_info->inmincid;
inimgid = ncvarid(inmincid, MIimage);
icvid = reshape_info->icvid;
/* Get input min and max for block */
get_block_min_and_max(reshape_info, block_start, block_count,
minmax_buffer, &minimum, &maximum);
/* Modify the icv if necessary */
if (reshape_info->do_block_normalization) {
(void) miicv_detach(icvid);
(void) miicv_setdbl(icvid, MI_ICV_IMAGE_MIN, minimum);
(void) miicv_setdbl(icvid, MI_ICV_IMAGE_MAX, maximum);
(void) miicv_setint(icvid, MI_ICV_USER_NORM, TRUE);
(void) miicv_setint(icvid, MI_ICV_DO_NORM, TRUE);
(void) miicv_attach(icvid, inmincid, inimgid);
}
/* Save the image max and min for the block */
for (iloop=0; iloop < 2; iloop++) {
/* Get varid and pointer to min or max value */
switch (iloop) {
case 0:
varname = MIimagemin;
extreme = &minimum;
break;
case 1:
varname = MIimagemax;
extreme = &maximum;
break;
}
/* Save the value */
ncopts = 0;
varid = ncvarid(reshape_info->outmincid, varname);
ncopts = NCOPTS_DEFAULT;
if (varid != MI_ERROR) {
(void) mitranslate_coords(reshape_info->outmincid,
reshape_info->outimgid, block_start,
varid, minmax_start);
(void) mivarput1(reshape_info->outmincid, varid,
minmax_start, NC_DOUBLE, NULL, extreme);
}
}
/* Calculate the pixel fill value */
*fillvalue = ((reshape_info->fillvalue == NOFILL) ? 0.0 :
reshape_info->fillvalue);
if ((reshape_info->output_datatype != NC_FLOAT) &&
(reshape_info->output_datatype != NC_DOUBLE) &&
(*fillvalue != FILL)) {
(void) miicv_inqdbl(icvid, MI_ICV_VALID_MIN, &valid_min);
(void) miicv_inqdbl(icvid, MI_ICV_VALID_MAX, &valid_max);
denom = maximum - minimum;
if (denom == 0.0) {
*fillvalue = valid_min;
}
else {
*fillvalue = (*fillvalue - minimum) *
(valid_max - valid_min) / denom + valid_min;
}
}
}
MNCAPI int
minc_save_data(int fd, void *dataptr, int datatype,
long st, long sz, long sy, long sx,
long ct, long cz, long cy, long cx)
{
nc_type nctype;
char *signstr;
int i;
int var_id;
int var_ndims;
int var_dims[MAX_NC_DIMS];
int icv;
long start[MI_S_NDIMS];
long count[MI_S_NDIMS];
int old_ncopts;
int r;
double min, max;
long slice_size;
long index;
int dtbytes; /* Length of datatype in bytes */
old_ncopts =get_ncopts();
set_ncopts(0);
var_id = ncvarid(fd, MIimage);
ncvarinq(fd, var_id, NULL, NULL, &var_ndims, var_dims, NULL);
set_ncopts(old_ncopts);
if (var_ndims < 2 || var_ndims > 4) {
return (MINC_STATUS_ERROR);
}
r = minc_simple_to_nc_type(datatype, &nctype, &signstr);
if (r == MINC_STATUS_ERROR) {
return (MINC_STATUS_ERROR);
}
dtbytes = nctypelen(nctype);
/* Update the image-min and image-max values */
if (ct > 0) {
slice_size = cz * cy * cx;
index = st;
for (i = 0; i < ct; i++) {
find_minmax((char *) dataptr + (dtbytes * slice_size * i),
slice_size, datatype, &min, &max);
mivarput1(fd, ncvarid(fd, MIimagemin), &index,
NC_DOUBLE, MI_SIGNED, &min);
mivarput1(fd, ncvarid(fd, MIimagemax), &index,
NC_DOUBLE, MI_SIGNED, &max);
index++;
}
}
else {
slice_size = cy * cx;
index = sz;
for (i = 0; i < cz; i++) {
find_minmax((char *) dataptr + (dtbytes * slice_size * i),
slice_size, datatype, &min, &max);
mivarput1(fd, ncvarid(fd, MIimagemin), &index,
NC_DOUBLE, MI_SIGNED, &min);
mivarput1(fd, ncvarid(fd, MIimagemax), &index,
NC_DOUBLE, MI_SIGNED, &max);
index++;
}
}
/* We want the data to wind up in t, x, y, z order. */
icv = miicv_create();
if (icv < 0) {
return (MINC_STATUS_ERROR);
}
r = miicv_setint(icv, MI_ICV_TYPE, nctype);
if (r < 0) {
return (MINC_STATUS_ERROR);
}
r = miicv_setstr(icv, MI_ICV_SIGN, signstr);
if (r < 0) {
return (MINC_STATUS_ERROR);
}
r = miicv_setint(icv, MI_ICV_DO_NORM, 1);
if (r < 0) {
return (MINC_STATUS_ERROR);
}
r = miicv_setint(icv, MI_ICV_DO_FILLVALUE, 1);
if (r < 0) {
return (MINC_STATUS_ERROR);
}
r = miicv_attach(icv, fd, var_id);
if (r < 0) {
return (MINC_STATUS_ERROR);
}
i = 0;
switch (var_ndims) {
case 4:
count[i] = ct;
start[i] = st;
i++;
/* fall through */
case 3:
count[i] = cz;
start[i] = sz;
i++;
/* fall through */
case 2:
count[i] = cy;
start[i] = sy;
i++;
count[i] = cx;
start[i] = sx;
i++;
break;
}
r = miicv_put(icv, start, count, dataptr);
if (r < 0) {
return (MINC_STATUS_ERROR);
}
miicv_detach(icv);
miicv_free(icv);
return (MINC_STATUS_OK);
}
int
main(int argc, char **argv)
{
/* NIFTI stuff */
nifti_image *nii_ptr;
nifti_image nii_rec;
int nii_dimids[MAX_NII_DIMS];
int nii_dir[MAX_NII_DIMS];
int nii_map[MAX_NII_DIMS];
unsigned long nii_lens[MAX_NII_DIMS];
int nii_ndims;
static int nifti_filetype;
static int nifti_datatype;
static int nifti_signed = 1;
/* MINC stuff */
int mnc_fd; /* MINC file descriptor */
nc_type mnc_type; /* MINC data type as read */
int mnc_ndims; /* MINC image dimension count */
int mnc_dimids[MAX_VAR_DIMS]; /* MINC image dimension identifiers */
long mnc_dlen; /* MINC dimension length value */
double mnc_dstep; /* MINC dimension step value */
int mnc_icv; /* MINC image conversion variable */
int mnc_vid; /* MINC Image variable ID */
long mnc_start[MAX_VAR_DIMS]; /* MINC data starts */
long mnc_count[MAX_VAR_DIMS]; /* MINC data counts */
int mnc_signed; /* MINC if output voxels are signed */
double real_range[2]; /* MINC real range (min, max) */
double input_valid_range[2]; /* MINC valid range (min, max) */
double output_valid_range[2]; /* Valid range of output data. */
double nifti_slope; /* Slope to be applied to output voxels. */
double nifti_inter; /* Intercept to be applied to output voxels. */
double total_valid_range; /* Overall valid range (max - min). */
double total_real_range; /* Overall real range (max - min). */
/* Other stuff */
char out_str[1024]; /* Big string for filename */
char att_str[1024]; /* Big string for attribute values */
int i; /* Generic loop counter the first */
int j; /* Generic loop counter the second */
char *str_ptr; /* Generic ASCIZ string pointer */
int r; /* Result code. */
static int vflag = 0; /* Verbose flag (default is quiet) */
static ArgvInfo argTable[] = {
{NULL, ARGV_HELP, NULL, NULL,
"Output voxel data type specification"},
{"-byte", ARGV_CONSTANT, (char *)DT_INT8, (char *)&nifti_datatype,
"Write voxel data in 8-bit signed integer format."},
{"-short", ARGV_CONSTANT, (char *)DT_INT16, (char *)&nifti_datatype,
"Write voxel data in 16-bit signed integer format."},
{"-int", ARGV_CONSTANT, (char *)DT_INT32, (char *)&nifti_datatype,
"Write voxel data in 32-bit signed integer format."},
{"-float", ARGV_CONSTANT, (char *)DT_FLOAT32, (char *)&nifti_datatype,
"Write voxel data in 32-bit floating point format."},
{"-double", ARGV_CONSTANT, (char *)DT_FLOAT64, (char *)&nifti_datatype,
"Write voxel data in 64-bit floating point format."},
{"-signed", ARGV_CONSTANT, (char *)1, (char *)&nifti_signed,
"Write integer voxel data in signed format."},
{"-unsigned", ARGV_CONSTANT, (char *)0, (char *)&nifti_signed,
"Write integer voxel data in unsigned format."},
{NULL, ARGV_HELP, NULL, NULL,
"Output file format specification"},
{"-dual", ARGV_CONSTANT, (char *)FT_NIFTI_DUAL,
(char *)&nifti_filetype,
"Write NIfTI-1 two-file format (.img and .hdr)"},
{"-ASCII", ARGV_CONSTANT, (char *)FT_NIFTI_ASCII,
(char *)&nifti_filetype,
"Write NIfTI-1 ASCII header format (.nia)"},
{"-nii", ARGV_CONSTANT, (char *)FT_NIFTI_SINGLE,
(char *)&nifti_filetype,
"Write NIfTI-1 one-file format (.nii)"},
{"-analyze", ARGV_CONSTANT, (char *)FT_ANALYZE,
(char *)&nifti_filetype,
"Write an Analyze two-file format file (.img and .hdr)"},
{NULL, ARGV_HELP, NULL, NULL,
"Other options"},
{"-quiet", ARGV_CONSTANT, (char *)0,
(char *)&vflag,
"Quiet operation"},
{"-verbose", ARGV_CONSTANT, (char *)1,
(char *)&vflag,
"Quiet operation"},
{NULL, ARGV_END, NULL, NULL, NULL}
};
ncopts = 0; /* Clear global netCDF error reporting flag */
/* Default NIfTI file type is "NII", single binary file
*/
nifti_filetype = FT_UNSPECIFIED;
nifti_datatype = DT_UNKNOWN;
if (ParseArgv(&argc, argv, argTable, 0) || (argc < 2)) {
fprintf(stderr, "Too few arguments\n");
return usage();
}
if (!nifti_signed) {
switch (nifti_datatype) {
case DT_INT8:
nifti_datatype = DT_UINT8;
break;
case DT_INT16:
nifti_datatype = DT_UINT16;
break;
case DT_INT32:
nifti_datatype = DT_UINT32;
break;
}
}
switch (nifti_datatype){
case DT_INT8:
case DT_UINT8:
mnc_type = NC_BYTE;
break;
case DT_INT16:
case DT_UINT16:
mnc_type = NC_SHORT;
break;
case DT_INT32:
case DT_UINT32:
mnc_type = NC_INT;
break;
case DT_FLOAT32:
mnc_type = NC_FLOAT;
break;
case DT_FLOAT64:
mnc_type = NC_DOUBLE;
break;
}
if (argc == 2) {
strcpy(out_str, argv[1]);
str_ptr = strrchr(out_str, '.');
if (str_ptr != NULL && !strcmp(str_ptr, ".mnc")) {
*str_ptr = '\0';
}
}
else if (argc == 3) {
strcpy(out_str, argv[2]);
str_ptr = strrchr(out_str, '.');
if (str_ptr != NULL) {
/* See if a recognized file extension was specified. If so,
* we trim it off and set the output file type if none was
* specified. If the extension is not recognized, assume
* that we will form the filename by just adding the right
* extension for the selected output format.
*/
if (!strcmp(str_ptr, ".nii")) {
if (nifti_filetype == FT_UNSPECIFIED) {
nifti_filetype = FT_NIFTI_SINGLE;
}
*str_ptr = '\0';
}
else if (!strcmp(str_ptr, ".img") ||
!strcmp(str_ptr, ".hdr")) {
if (nifti_filetype == FT_UNSPECIFIED) {
nifti_filetype = FT_NIFTI_DUAL;
}
*str_ptr = '\0';
}
else if (!strcmp(str_ptr, ".nia")) {
if (nifti_filetype == FT_UNSPECIFIED) {
nifti_filetype = FT_NIFTI_ASCII;
}
*str_ptr = '\0';
}
}
}
else {
fprintf(stderr, "Filename argument required\n");
return usage();
}
/* Open the MINC file. It needs to exist.
*/
mnc_fd = miopen(argv[1], NC_NOWRITE);
if (mnc_fd < 0) {
fprintf(stderr, "Can't find input file '%s'\n", argv[1]);
return (-1);
}
/* Find the MINC image variable. If we can't find it, there is no
* further processing possible...
*/
mnc_vid = ncvarid(mnc_fd, MIimage);
if (mnc_vid < 0) {
fprintf(stderr, "Can't locate the image variable (mnc_vid=%d)\n", mnc_vid);
return (-1);
}
/* Find out about the MINC image variable - specifically, how many
* dimensions, and which dimensions.
*/
r = ncvarinq(mnc_fd, mnc_vid, NULL, NULL, &mnc_ndims, mnc_dimids, NULL);
if (r < 0) {
fprintf(stderr, "Can't read information from image variable\n");
return (-1);
}
if (mnc_ndims > MAX_NII_DIMS) {
fprintf(stderr, "NIfTI-1 files may contain at most %d dimensions\n",
MAX_NII_DIMS);
return (-1);
}
/* Initialize the NIfTI structure
*/
nii_ptr = &nii_rec;
init_nifti_header(nii_ptr);
/* For now we just use the mnc2nii command line as the description
* field. Probably we should use something better, perhaps a
* combination of some other standard MINC fields that might
* provide more information.
*/
str_ptr = nii_ptr->descrip;
for (i = 0; i < argc; i++) {
char *arg_ptr = argv[i];
if ((str_ptr - nii_ptr->descrip) >= MAX_NII_DESCRIP) {
break;
}
if (i != 0) {
*str_ptr++ = ' ';
}
while (*arg_ptr != '\0' &&
(str_ptr - nii_ptr->descrip) < MAX_NII_DESCRIP) {
*str_ptr++ = *arg_ptr++;
}
*str_ptr = '\0';
}
nii_ptr->fname = malloc(strlen(out_str) + 4 + 1);
nii_ptr->iname = malloc(strlen(out_str) + 4 + 1);
strcpy(nii_ptr->fname, out_str);
strcpy(nii_ptr->iname, out_str);
switch (nifti_filetype) {
case FT_ANALYZE:
strcat(nii_ptr->fname, ".hdr");
strcat(nii_ptr->iname, ".img");
break;
case FT_NIFTI_SINGLE:
strcat(nii_ptr->fname, ".nii");
strcat(nii_ptr->iname, ".nii");
break;
case FT_NIFTI_DUAL:
strcat(nii_ptr->fname, ".hdr");
strcat(nii_ptr->iname, ".img");
break;
case FT_NIFTI_ASCII:
strcat(nii_ptr->fname, ".nia");
strcat(nii_ptr->iname, ".nia");
break;
default:
fprintf(stderr, "Unknown output file type %d\n", nifti_filetype);
return (-1);
}
/* Get real voxel range for the input file.
*/
miget_image_range(mnc_fd, real_range);
/* Get the actual valid voxel value range.
*/
miget_valid_range(mnc_fd, mnc_vid, input_valid_range);
/* Find the default range for the output type. Our output file
* will use the full legal range of the output type if it is
* an integer.
*/
if (nifti_datatype == DT_UNKNOWN) {
nii_ptr->datatype = DT_FLOAT32; /* Default */
mnc_type = NC_FLOAT;
mnc_signed = 1;
}
else {
nii_ptr->datatype = nifti_datatype;
mnc_signed = nifti_signed;
}
if (vflag) {
fprintf(stderr, "MINC type %d signed %d\n", mnc_type, mnc_signed);
}
miget_default_range(mnc_type, mnc_signed, output_valid_range);
total_valid_range = input_valid_range[1] - input_valid_range[0];
total_real_range = real_range[1] - real_range[0];
if ((output_valid_range[1] - output_valid_range[0]) > total_valid_range) {
/* Empirically, forcing the valid range to be the nearest power
* of two greater than the existing valid range seems to improve
* the behavior of the conversion. This is at least in part because
* of the limited precision of the NIfTI-1 voxel scaling fields.
*/
double new_range = nearest_power_of_two(total_valid_range);
if (new_range - 1.0 >= total_valid_range) {
new_range -= 1.0;
}
if (output_valid_range[1] > total_valid_range) {
output_valid_range[0] = 0;
output_valid_range[1] = new_range;
}
else {
output_valid_range[1] = output_valid_range[0] + new_range;
}
}
else {
/* The new range can't fully represent the input range. Use the
* full available range, and warn the user that they may have a
* problem.
*/
printf("WARNING: Range of input exceeds range of output format.\n");
}
if (vflag) {
printf("Real range: %f %f Input valid range: %f %f Output valid range: %f %f\n",
real_range[0], real_range[1],
input_valid_range[0], input_valid_range[1],
output_valid_range[0], output_valid_range[1]);
}
/* If the output type is not floating point, we may need to scale the
* voxel values.
*/
if (mnc_type != NC_FLOAT && mnc_type != NC_DOUBLE) {
/* Figure out how to map pixel values into the range of the
* output datatype.
*/
nifti_slope = ((real_range[1] - real_range[0]) /
(output_valid_range[1] - output_valid_range[0]));
if (nifti_slope == 0.0) {
nifti_slope = 1.0;
}
nifti_inter = real_range[0] - (output_valid_range[0] * nifti_slope);
/* One problem with NIfTI-1 is the limited precision of the
* scl_slope and scl_inter fields (they are just 32-bits). So
* we look for possible issues and warn about that here.
*/
if (nifti_inter != (float) nifti_inter ||
nifti_slope != (float) nifti_slope) {
double epsilon_i = nifti_inter - (float) nifti_inter;
double epsilon_s = nifti_slope - (float) nifti_slope;
/* If the loss in precision is more than one part per thousand
* of the real range, flag this as a problem!
*/
if ((epsilon_i > total_real_range / 1.0e3) ||
(epsilon_s > total_real_range / 1.0e3)) {
fprintf(stderr, "ERROR: Slope and intercept cannot be represented in the NIfTI-1 header.\n");
fprintf(stderr, " slope %f (%f), intercept %f (%f)\n",
nifti_slope, (float) nifti_slope,
nifti_inter, (float) nifti_inter);
return (-1);
}
}
}
else {
nifti_slope = 0.0;
}
nii_ptr->scl_slope = nifti_slope;
nii_ptr->scl_inter = nifti_inter;
nii_ptr->nvox = 1; /* Initial value for voxel count */
/* Find all of the dimensions of the MINC file, in the order they
* will be listed in the NIfTI-1/Analyze file. We use this to build
* a map for restructuring the data according to the normal rules
* of NIfTI-1.
*/
nii_ndims = 0;
for (i = 0; i < MAX_NII_DIMS; i++) {
if (dimnames[i] == NULL) {
nii_dimids[nii_ndims] = -1;
continue;
}
nii_dimids[nii_ndims] = ncdimid(mnc_fd, dimnames[i]);
if (nii_dimids[nii_ndims] == -1) {
continue;
}
/* Make sure the dimension is actually used to define the image.
*/
for (j = 0; j < mnc_ndims; j++) {
if (nii_dimids[nii_ndims] == mnc_dimids[j]) {
nii_map[nii_ndims] = j;
break;
}
}
if (j < mnc_ndims) {
mnc_dlen = 1;
mnc_dstep = 0;
ncdiminq(mnc_fd, nii_dimids[nii_ndims], NULL, &mnc_dlen);
ncattget(mnc_fd, ncvarid(mnc_fd, dimnames[i]), MIstep, &mnc_dstep);
if (mnc_dstep < 0) {
nii_dir[nii_ndims] = -1;
mnc_dstep = -mnc_dstep;
}
else {
nii_dir[nii_ndims] = 1;
}
nii_lens[nii_ndims] = mnc_dlen;
nii_ndims++;
}
nii_ptr->dim[dimmap[i]] = (int) mnc_dlen;
nii_ptr->nvox *= mnc_dlen;
nii_ptr->pixdim[dimmap[i]] = (float) mnc_dstep;
}
/* Here we do some "post-processing" of the results. Make certain that
* the nt value is never zero, and make certain that ndim is set to
* 4 if there is a time dimension and 5 if there is a vector dimension
*/
if (nii_ptr->dim[3] > 1 && nii_ndims < 4) {
nii_ndims = 4;
}
if (nii_ptr->dim[4] > 1) {
nii_ptr->intent_code = NIFTI_INTENT_VECTOR;
nii_ndims = 5;
}
nii_ptr->ndim = nii_ndims; /* Total number of dimensions in file */
nii_ptr->nx = nii_ptr->dim[0];
nii_ptr->ny = nii_ptr->dim[1];
nii_ptr->nz = nii_ptr->dim[2];
nii_ptr->nt = nii_ptr->dim[3];
nii_ptr->nu = nii_ptr->dim[4];
nii_ptr->dx = nii_ptr->pixdim[0];
nii_ptr->dy = nii_ptr->pixdim[1];
nii_ptr->dz = nii_ptr->pixdim[2];
nii_ptr->dt = nii_ptr->pixdim[3];
nii_ptr->du = 1; /* MINC files don't define a sample size for a vector_dimension */
nii_ptr->nifti_type = nifti_filetype;
/* Load the direction_cosines and start values into the NIfTI-1
* sform structure.
*
*/
for (i = 0; i < MAX_SPACE_DIMS; i++) {
int id = ncvarid(mnc_fd, mnc_spatial_names[i]);
double start;
double step;
double dircos[MAX_SPACE_DIMS];
int tmp;
if (id < 0) {
continue;
}
/* Set default values */
start = 0.0;
step = 1.0;
dircos[DIM_X] = dircos[DIM_Y] = dircos[DIM_Z] = 0.0;
dircos[i] = 1.0;
miattget(mnc_fd, id, MIstart, NC_DOUBLE, 1, &start, &tmp);
miattget(mnc_fd, id, MIstep, NC_DOUBLE, 1, &step, &tmp);
miattget(mnc_fd, id, MIdirection_cosines, NC_DOUBLE, MAX_SPACE_DIMS,
dircos, &tmp);
ncdiminq(mnc_fd, ncdimid(mnc_fd, mnc_spatial_names[i]), NULL,
&mnc_dlen);
if (step < 0) {
step = -step;
start = start - step * (mnc_dlen - 1);
}
nii_ptr->sto_xyz.m[0][i] = step * dircos[0];
nii_ptr->sto_xyz.m[1][i] = step * dircos[1];
nii_ptr->sto_xyz.m[2][i] = step * dircos[2];
nii_ptr->sto_xyz.m[0][3] += start * dircos[0];
nii_ptr->sto_xyz.m[1][3] += start * dircos[1];
nii_ptr->sto_xyz.m[2][3] += start * dircos[2];
miattgetstr(mnc_fd, id, MIspacetype, sizeof(att_str), att_str);
/* Try to set the S-transform code correctly.
*/
if (!strcmp(att_str, MI_TALAIRACH)) {
nii_ptr->sform_code = NIFTI_XFORM_TALAIRACH;
}
else if (!strcmp(att_str, MI_CALLOSAL)) {
/* TODO: Not clear what do do here... */
nii_ptr->sform_code = NIFTI_XFORM_SCANNER_ANAT;
}
else { /* MI_NATIVE or unknown */
nii_ptr->sform_code = NIFTI_XFORM_SCANNER_ANAT;
}
}
/* So the last row is right... */
nii_ptr->sto_xyz.m[3][0] = 0.0;
nii_ptr->sto_xyz.m[3][1] = 0.0;
nii_ptr->sto_xyz.m[3][2] = 0.0;
nii_ptr->sto_xyz.m[3][3] = 1.0;
nii_ptr->sto_ijk = nifti_mat44_inverse(nii_ptr->sto_xyz);
nifti_datatype_sizes(nii_ptr->datatype,
&nii_ptr->nbyper, &nii_ptr->swapsize);
if (vflag) {
nifti_image_infodump(nii_ptr);
}
/* Now load the actual MINC data. */
nii_ptr->data = malloc(nii_ptr->nbyper * nii_ptr->nvox);
if (nii_ptr->data == NULL) {
fprintf(stderr, "Out of memory.\n");
return (-1);
}
mnc_icv = miicv_create();
miicv_setint(mnc_icv, MI_ICV_TYPE, mnc_type);
miicv_setstr(mnc_icv, MI_ICV_SIGN, (mnc_signed) ? MI_SIGNED : MI_UNSIGNED);
miicv_setdbl(mnc_icv, MI_ICV_VALID_MAX, output_valid_range[1]);
miicv_setdbl(mnc_icv, MI_ICV_VALID_MIN, output_valid_range[0]);
miicv_setdbl(mnc_icv, MI_ICV_IMAGE_MAX, real_range[1]);
miicv_setdbl(mnc_icv, MI_ICV_IMAGE_MIN, real_range[0]);
miicv_setdbl(mnc_icv, MI_ICV_DO_NORM, TRUE);
miicv_setdbl(mnc_icv, MI_ICV_USER_NORM, TRUE);
miicv_attach(mnc_icv, mnc_fd, mnc_vid);
/* Read in the entire hyperslab from the file.
*/
for (i = 0; i < mnc_ndims; i++) {
ncdiminq(mnc_fd, mnc_dimids[i], NULL, &mnc_count[i]);
mnc_start[i] = 0;
}
r = miicv_get(mnc_icv, mnc_start, mnc_count, nii_ptr->data);
if (r < 0) {
fprintf(stderr, "Read error\n");
return (-1);
}
/* Shut down the MINC stuff now that it has done its work.
*/
miicv_detach(mnc_icv);
miicv_free(mnc_icv);
miclose(mnc_fd);
if (vflag) {
/* Debugging stuff - just to check the contents of these arrays.
*/
for (i = 0; i < nii_ndims; i++) {
printf("%d: %ld %d %d\n",
i, nii_lens[i], nii_map[i], nii_dir[i]);
}
printf("bytes per voxel %d\n", nii_ptr->nbyper);
printf("# of voxels %ld\n", nii_ptr->nvox);
}
/* Rearrange the data to correspond to the NIfTI dimension ordering.
*/
restructure_array(nii_ndims,
nii_ptr->data,
nii_lens,
nii_ptr->nbyper,
nii_map,
nii_dir);
if (vflag) {
/* More debugging stuff - check coordinate transform.
*/
test_xform(nii_ptr->sto_xyz, 0, 0, 0);
test_xform(nii_ptr->sto_xyz, 10, 0, 0);
test_xform(nii_ptr->sto_xyz, 0, 10, 0);
test_xform(nii_ptr->sto_xyz, 0, 0, 10);
test_xform(nii_ptr->sto_xyz, 10, 10, 10);
}
if (vflag) {
fprintf(stdout, "Writing NIfTI-1 file...");
}
nifti_image_write(nii_ptr);
if (vflag) {
fprintf(stdout, "done.\n");
}
return (0);
}
MNCAPI int
minc_load_data(char *path, void *dataptr, int datatype,
long *ct, long *cz, long *cy, long *cx,
double *dt, double *dz, double *dy, double *dx,
void **infoptr)
{
int fd; /* MINC file descriptor */
nc_type nctype; /* netCDF type */
char *signstr; /* MI_SIGNED or MI_UNSIGNED */
int length;
int dim_id[MI_S_NDIMS];
long dim_len[MI_S_NDIMS];
int i, j; /* Generic loop counters */
int var_id;
int var_ndims;
int var_dims[MAX_NC_DIMS];
int icv; /* MINC image conversion variable */
long start[MI_S_NDIMS];
long count[MI_S_NDIMS];
size_t ucount[MI_S_NDIMS];
int dir[MI_S_NDIMS]; /* Dimension "directions" */
int map[MI_S_NDIMS]; /* Dimension mapping */
int old_ncopts; /* For storing the old state of ncopts */
double *p_dtmp;
long *p_ltmp;
struct file_info *p_file;
struct att_info *p_att;
int r; /* Generic return code */
*infoptr = NULL;
fd = miopen(path, NC_NOWRITE);
if (fd < 0) {
return (MINC_STATUS_ERROR);
}
old_ncopts =get_ncopts();
set_ncopts(0);
for (i = 0; i < MI_S_NDIMS; i++) {
dim_id[i] = ncdimid(fd, minc_dimnames[i]);
if (dim_id[i] >= 0) {
ncdiminq(fd, dim_id[i], NULL, &dim_len[i]);
var_id = ncvarid(fd, minc_dimnames[i]);
ncattinq(fd, var_id, MIstep, &nctype, &length);
switch (i) {
case MI_S_T:
p_ltmp = ct;
p_dtmp = dt;
break;
case MI_S_X:
p_ltmp = cx;
p_dtmp = dx;
break;
case MI_S_Y:
p_ltmp = cy;
p_dtmp = dy;
break;
case MI_S_Z:
p_ltmp = cz;
p_dtmp = dz;
break;
default:
return (MINC_STATUS_ERROR);
}
if (nctype == NC_DOUBLE && length == 1) {
ncattget(fd, var_id, MIstep, p_dtmp);
}
else {
*p_dtmp = 0; /* Unknown/not set */
}
*p_ltmp = dim_len[i];
}
else {
dim_len[i] = 0;
}
}
set_ncopts(old_ncopts);
var_id = ncvarid(fd, MIimage);
ncvarinq(fd, var_id, NULL, &nctype, &var_ndims, var_dims, NULL);
if (var_ndims != 3 && var_ndims != 4) {
return (MINC_STATUS_ERROR);
}
/* We want the data to wind up in t, x, y, z order. */
for (i = 0; i < MI_S_NDIMS; i++) {
map[i] = -1;
}
for (i = 0; i < var_ndims; i++) {
if (var_dims[i] == dim_id[MI_S_T]) {
map[MI_S_T] = i;
}
else if (var_dims[i] == dim_id[MI_S_X]) {
map[MI_S_X] = i;
}
else if (var_dims[i] == dim_id[MI_S_Y]) {
map[MI_S_Y] = i;
}
else if (var_dims[i] == dim_id[MI_S_Z]) {
map[MI_S_Z] = i;
}
}
icv = miicv_create();
minc_simple_to_nc_type(datatype, &nctype, &signstr);
miicv_setint(icv, MI_ICV_TYPE, nctype);
miicv_setstr(icv, MI_ICV_SIGN, signstr);
miicv_attach(icv, fd, var_id);
for (i = 0; i < var_ndims; i++) {
start[i] = 0;
}
for (i = 0; i < MI_S_NDIMS; i++) {
if (map[i] >= 0) {
count[map[i]] = dim_len[i];
}
}
r = miicv_get(icv, start, count, dataptr);
if (r < 0) {
return (MINC_STATUS_ERROR);
}
if (map[MI_S_T] >= 0) {
if (*dt < 0) {
dir[MI_S_T] = -1;
*dt = -*dt;
}
else {
dir[MI_S_T] = 1;
}
}
if (map[MI_S_X] >= 0) {
if (*dx < 0) {
dir[MI_S_X] = -1;
*dx = -*dx;
}
else {
dir[MI_S_X] = 1;
}
}
if (map[MI_S_Y] >= 0) {
if (*dy < 0) {
dir[MI_S_Y] = -1;
*dy = -*dy;
}
else {
dir[MI_S_Y] = 1;
}
}
if (map[MI_S_Z] >= 0) {
if (*dz < 0) {
dir[MI_S_Z] = -1;
*dz = -*dz;
}
else {
dir[MI_S_Z] = 1;
}
}
if (var_ndims == 3) {
for (i = 1; i < MI_S_NDIMS; i++) {
map[i-1] = map[i];
dir[i-1] = dir[i];
}
}
j = 0;
for (i = 0; i < MI_S_NDIMS; i++) {
if (dim_len[i] > 0) {
ucount[j++] = dim_len[i];
}
}
restructure_array(var_ndims, dataptr, ucount, nctypelen(nctype),
map, dir);
miicv_detach(icv);
miicv_free(icv);
old_ncopts =get_ncopts();
set_ncopts(0);
/* Generate the complete infoptr array.
* This is essentially an in-memory copy of the variables and attributes
* in the file.
*/
p_file = (struct file_info *) malloc(sizeof (struct file_info));
ncinquire(fd, &p_file->file_ndims, &p_file->file_nvars,
&p_file->file_natts, NULL);
p_file->file_atts = (struct att_info *) malloc(sizeof (struct att_info) *
p_file->file_natts);
p_file->file_vars = (struct var_info *) malloc(sizeof (struct var_info) *
p_file->file_nvars);
for (i = 0; i < p_file->file_natts; i++) {
p_att = &p_file->file_atts[i];
ncattname(fd, NC_GLOBAL, i, p_att->att_name);
ncattinq(fd, NC_GLOBAL,
p_att->att_name,
&p_att->att_type,
&p_att->att_len);
p_att->att_val = malloc(p_att->att_len * nctypelen(p_att->att_type));
ncattget(fd, NC_GLOBAL, p_att->att_name, p_att->att_val);
}
for (i = 0; i < p_file->file_nvars; i++) {
struct var_info *p_var = &p_file->file_vars[i];
ncvarinq(fd, i,
p_var->var_name,
&p_var->var_type,
&p_var->var_ndims,
p_var->var_dims,
&p_var->var_natts);
p_var->var_atts = malloc(p_var->var_natts *
sizeof (struct att_info));
if (ncdimid(fd, p_var->var_name) >= 0) {
/* It's a dimension variable, have to treat it specially... */
}
for (j = 0; j < p_var->var_natts; j++) {
p_att = &p_var->var_atts[j];
ncattname(fd, i, j, p_att->att_name);
ncattinq(fd, i,
p_att->att_name,
&p_att->att_type,
&p_att->att_len);
p_att->att_val = malloc(p_att->att_len * nctypelen(p_att->att_type));
ncattget(fd, i, p_att->att_name, p_att->att_val);
}
}
*infoptr = p_file;
set_ncopts(old_ncopts);
miclose(fd);
return (MINC_STATUS_OK);
}
int
test7(struct testinfo *ip, struct dimdef *dims, int ndims)
{
size_t total;
long coords[3];
long lengths[3];
void *buf_ptr;
int *int_ptr;
int i, j, k;
int stat;
int icv;
total = 1;
for (i = 0; i < ndims; i++) {
total *= dims[i].length;
}
buf_ptr = malloc(total * sizeof (float));
if (buf_ptr == NULL) {
fprintf(stderr, "Oops, malloc failed\n");
return (-1);
}
icv = miicv_create();
if (icv < 0) {
FUNC_ERROR("miicv_create");
}
/* Test range conversion. */
stat = miicv_setint(icv, MI_ICV_DO_DIM_CONV, 0);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_setint(icv, MI_ICV_DO_RANGE, 1);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_setstr(icv, MI_ICV_SIGN, MI_UNSIGNED);
if (stat < 0) {
FUNC_ERROR("miicv_setstr");
}
stat = miicv_setint(icv, MI_ICV_TYPE, NC_INT);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_setint(icv, MI_ICV_VALID_MAX, 1000);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_setint(icv, MI_ICV_VALID_MIN, -1000);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_attach(icv, ip->fd, ip->imgid);
if (stat < 0) {
FUNC_ERROR("miicv_attach");
}
coords[TST_X] = 0;
coords[TST_Y] = 0;
coords[TST_Z] = 0;
lengths[TST_X] = dims[TST_X].length;
lengths[TST_Y] = dims[TST_Y].length;
lengths[TST_Z] = dims[TST_Z].length;
stat = miicv_get(icv, coords, lengths, buf_ptr);
if (stat < 0) {
FUNC_ERROR("miicv_get");
}
int_ptr = (int *) buf_ptr;
for (i = 0; i < dims[TST_X].length; i++) {
for (j = 0; j < dims[TST_Y].length; j++) {
for (k = 0; k < dims[TST_Z].length; k++, int_ptr++) {
int tmp = (i * 10000) + (j * 100) + (k);
int rng = (XSIZE * 10000) / 1000;
/* Round tmp properly. */
tmp = (tmp + (rng / 2)) / rng;
if (*int_ptr != tmp) {
fprintf(stderr, "5. Data error at (%d,%d,%d) %d != %d\n",
i,j,k, *int_ptr, tmp);
errors++;
}
}
}
}
stat = miicv_detach(icv);
if (stat < 0) {
FUNC_ERROR("miicv_detach");
}
/* Free the ICV */
stat = miicv_free(icv);
if (stat < 0) {
FUNC_ERROR("miicv_free");
}
free(buf_ptr);
return (0);
}
int
test6(struct testinfo *ip, struct dimdef *dims, int ndims)
{
size_t total;
long coords[3];
long lengths[3];
void *buf_ptr;
int *int_ptr;
int i, j, k;
int stat;
int icv;
total = 1;
total *= dims[TST_X].length;
total *= dims[TST_Y].length - YBOOST;
total *= dims[TST_Z].length - ZBOOST;
buf_ptr = malloc(total * sizeof (int));
if (buf_ptr == NULL) {
fprintf(stderr, "Oops, malloc failed\n");
return (-1);
}
icv = miicv_create();
if (icv < 0) {
FUNC_ERROR("miicv_create");
}
/* Now try reading the image with reduced size.
*/
stat = miicv_setint(icv, MI_ICV_BDIM_SIZE, dims[TST_Y].length - YBOOST);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_setint(icv, MI_ICV_ADIM_SIZE, dims[TST_Z].length - ZBOOST);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_setint(icv, MI_ICV_DO_DIM_CONV, 1);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_attach(icv, ip->fd, ip->imgid);
if (stat < 0) {
FUNC_ERROR("miicv_attach");
}
coords[TST_X] = 0;
coords[TST_Y] = 0;
coords[TST_Z] = 0;
lengths[TST_X] = dims[TST_X].length;
lengths[TST_Y] = dims[TST_Y].length - YBOOST;
lengths[TST_Z] = dims[TST_Z].length - ZBOOST;
stat = miicv_get(icv, coords, lengths, buf_ptr);
if (stat < 0) {
FUNC_ERROR("miicv_get");
}
int_ptr = (int *) buf_ptr;
for (i = 0; i < dims[TST_X].length; i++) {
for (j = 0; j < dims[TST_Y].length - YBOOST; j++) {
for (k = 0; k < dims[TST_Z].length - ZBOOST; k++, int_ptr++) {
int tmp;
tmp = (i * 10000) + (j * 100) + (k);
if (*int_ptr != (int) tmp) {
fprintf(stderr, "4. Data error at (%d,%d,%d) %d != %d\n",
i,j,k, *int_ptr, tmp);
errors++;
}
}
}
}
stat = miicv_detach(icv);
if (stat < 0) {
FUNC_ERROR("miicv_detach");
}
stat = miicv_free(icv);
if (stat < 0) {
FUNC_ERROR("miicv_free");
}
free(buf_ptr);
return (0);
}
int
test5(struct testinfo *ip, struct dimdef *dims, int ndims)
{
/* Get the same variable again, but this time use an ICV to scale it.
*/
size_t total;
long coords[3];
long lengths[3];
void *buf_ptr;
int *int_ptr;
int i, j, k;
int stat;
int icv;
total = 1;
total *= dims[TST_X].length;
total *= dims[TST_Y].length + YBOOST;
total *= dims[TST_Z].length + ZBOOST;
buf_ptr = malloc(total * sizeof (int));
if (buf_ptr == NULL) {
fprintf(stderr, "Oops, malloc failed\n");
return (-1);
}
icv = miicv_create();
if (icv < 0) {
FUNC_ERROR("miicv_create");
}
/* Now set up a dimension conversion. */
stat = miicv_setint(icv, MI_ICV_DO_NORM, 0);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_setint(icv, MI_ICV_DO_RANGE, 0);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_setint(icv, MI_ICV_TYPE, NC_INT);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_setint(icv, MI_ICV_YDIM_DIR, MI_ICV_NEGATIVE);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_setint(icv, MI_ICV_ZDIM_DIR, MI_ICV_NEGATIVE);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_setint(icv, MI_ICV_BDIM_SIZE, dims[TST_Y].length + YBOOST);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_setint(icv, MI_ICV_ADIM_SIZE, dims[TST_Z].length + ZBOOST);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_setint(icv, MI_ICV_DO_DIM_CONV, 1);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_attach(icv, ip->fd, ip->imgid);
if (stat < 0) {
FUNC_ERROR("miicv_attach");
}
coords[TST_X] = 0;
coords[TST_Y] = 0;
coords[TST_Z] = 0;
lengths[TST_X] = dims[TST_X].length;
lengths[TST_Y] = dims[TST_Y].length + YBOOST;
lengths[TST_Z] = dims[TST_Z].length + ZBOOST;
stat = miicv_get(icv, coords, lengths, buf_ptr);
if (stat < 0) {
FUNC_ERROR("miicv_get");
}
int_ptr = (int *) buf_ptr;
for (i = 0; i < dims[TST_X].length; i++) {
for (j = 0; j < dims[TST_Y].length + YBOOST; j++) {
for (k = 0; k < dims[TST_Z].length + ZBOOST; k++, int_ptr++) {
int x;
int y;
int z;
int tmp;
if (j < YBOOST/2 || j >= dims[TST_Y].length + YBOOST/2)
continue;
if (k < ZBOOST/2 || k >= dims[TST_Z].length + ZBOOST/2)
continue;
x = i;
y = (YSIZE + YBOOST - 1) - j;
z = (ZSIZE + ZBOOST - 1) - k;
y -= YBOOST / 2;
z -= ZBOOST / 2;
tmp = (x * 10000) + (y * 100) + (z);
if (*int_ptr != (int) tmp) {
fprintf(stderr, "3. Data error at (%d,%d,%d) %d != %d\n",
i,j,k, *int_ptr, tmp);
errors++;
}
}
}
}
stat = miicv_detach(icv);
if (stat < 0) {
FUNC_ERROR("miicv_detach");
}
stat = miicv_free(icv);
if (stat < 0) {
FUNC_ERROR("miicv_free");
}
free(buf_ptr);
return (0);
}
int
test4(struct testinfo *ip, struct dimdef *dims, int ndims)
{
/* Get the same variable again, but this time use an ICV to scale it.
*/
size_t total;
long coords[3];
long lengths[3];
double range[2];
void *buf_ptr;
float *flt_ptr;
int i, j, k;
int stat;
int icv;
double dbl;
total = 1;
for (i = 0; i < ndims; i++) {
total *= dims[i].length;
}
buf_ptr = malloc(total * sizeof (float));
if (buf_ptr == NULL) {
fprintf(stderr, "Oops, malloc failed\n");
return (-1);
}
coords[TST_X] = 0;
coords[TST_Y] = 0;
coords[TST_Z] = 0;
lengths[TST_X] = dims[TST_X].length;
lengths[TST_Y] = dims[TST_Y].length;
lengths[TST_Z] = dims[TST_Z].length;
icv = miicv_create();
if (icv < 0) {
FUNC_ERROR("miicv_create");
}
stat = miicv_setint(icv, MI_ICV_TYPE, NC_FLOAT);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_setint(icv, MI_ICV_DO_NORM, 1);
if (stat < 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_attach(icv, ip->fd, ip->imgid);
if (stat < 0) {
FUNC_ERROR("miicv_attach");
}
/* This next call _should_ fail, since the ICV has been attached.
*/
stat = miicv_setint(icv, MI_ICV_DO_NORM, 0);
if (stat >= 0) {
FUNC_ERROR("miicv_setint");
}
stat = miicv_inqdbl(icv, MI_ICV_DO_NORM, &dbl);
if (stat < 0) {
FUNC_ERROR("miicv_inqdbl");
}
if (dbl != 1.0) {
fprintf(stderr, "miicv_inqdbl: Bad value returned\n");
errors++;
}
stat = miicv_get(icv, coords, lengths, buf_ptr);
if (stat < 0) {
FUNC_ERROR("miicv_get");
}
stat = miget_image_range(ip->fd, range);
if (stat < 0) {
FUNC_ERROR("miget_image_range");
}
if (range[0] != -(XSIZE * 100000.0) || range[1] != (XSIZE * 100000.00)) {
fprintf(stderr, "miget_image_range: bad result\n");
errors++;
}
stat = miget_valid_range(ip->fd, ip->imgid, range);
if (stat < 0) {
FUNC_ERROR("miget_valid_range");
}
if (range[0] != -(XSIZE * 10000.0) || range[1] != (XSIZE * 10000.0)) {
fprintf(stderr, "miget_valid_range: bad result\n");
errors++;
}
flt_ptr = (float *) buf_ptr;
for (i = 0; i < dims[TST_X].length; i++) {
for (j = 0; j < dims[TST_Y].length; j++) {
for (k = 0; k < dims[TST_Z].length; k++) {
float tmp = (i * 10000) + (j * 100) + k;
if (*flt_ptr != (float) tmp * 10.0) {
fprintf(stderr, "2. Data error at (%d,%d,%d) %f != %f\n",
i,j,k, *flt_ptr, tmp);
errors++;
}
flt_ptr++;
}
}
}
stat = miicv_detach(icv);
if (stat < 0) {
FUNC_ERROR("miicv_detach");
}
/* Try it again, to make certain we fail gracefully.
*/
stat = miicv_detach(icv);
if (stat < 0) {
FUNC_ERROR("miicv_detach");
}
/* Try to detach a completely random number.
*/
stat = miicv_detach(rand());
if (stat >= 0) {
FUNC_ERROR("miicv_detach");
}
stat = miicv_free(icv);
if (stat < 0) {
FUNC_ERROR("miicv_free");
}
free(buf_ptr);
return (0);
}