int main(int argc, char *argv[])
{
char **input_files;
char *output_file;
char *arg_string;
int num_input_files;
int inmincid;
Loop_Options *loop_options;
Program_Data program_data;
/* Save time stamp and args */
arg_string = time_stamp(argc, argv);
/* Get arguments */
if (ParseArgv(&argc, argv, argTable, 0) || (argc < 3)) {
(void) fprintf(stderr,
"\nUsage: %s [options] <in1.mnc> [...] <out.mnc>\n",
argv[0]);
(void) fprintf(stderr,
" %s -help\n\n",
argv[0]);
exit(EXIT_FAILURE);
}
input_files = &argv[1];
num_input_files = argc - 2;
output_file = argv[argc-1];
/* Open the first input file and get the vector length */
inmincid = miopen(input_files[0], NC_NOWRITE);
if (get_vector_length(inmincid) > 1) {
(void) fprintf(stderr, "Input file %s is not a scalar file\n",
input_files[0]);
exit(EXIT_FAILURE);
}
/* Set up looping options */
loop_options = create_loop_options();
set_loop_clobber(loop_options, clobber);
set_loop_verbose(loop_options, verbose);
#if MINC2
set_loop_v2format(loop_options, v2format);
#endif /* MINC2 */
set_loop_datatype(loop_options, datatype, is_signed,
valid_range[0], valid_range[1]);
set_loop_output_vector_size(loop_options, num_input_files);
set_loop_buffer_size(loop_options, (long) buffer_size * 1024);
set_loop_first_input_mincid(loop_options, inmincid);
set_loop_accumulate(loop_options, TRUE, 0, NULL, NULL);
/* Do loop */
voxel_loop(num_input_files, input_files, 1, &output_file,
arg_string, loop_options,
do_makevector, (void *) &program_data);
exit(EXIT_SUCCESS);
}
/* Main program */
int main(int argc, char *argv[]){
char **infiles, **outfiles;
int nfiles, nout;
char *arg_string;
Loop_Options *loop_options;
char *pname;
int i;
ident_t ident;
scalar_t scalar;
/* Save time stamp and args */
arg_string = time_stamp(argc, argv);
/* Get arguments */
pname = argv[0];
if (ParseArgv(&argc, argv, argTable, 0) || (argc < 2)) {
(void) fprintf(stderr,
"\nUsage: %s [options] [<in1.mnc> ...] <out.mnc>\n",
pname);
(void) fprintf(stderr,
" %s -help\n\n", pname);
exit(EXIT_FAILURE);
}
/* Get output file names */
nout = (Output_list == NULL ? 1 : Output_list_size);
outfiles = malloc(nout * sizeof(*outfiles));
if (Output_list == NULL) {
outfiles[0] = argv[argc-1];
}
else {
for (i=0; i < Output_list_size; i++) {
outfiles[i] = Output_list[i].file;
}
}
/* check for output files */
for (i=0; i < nout; i++){
if(access(outfiles[i], F_OK) == 0 && !clobber){
fprintf(stderr, "%s: %s exists, use -clobber to overwrite\n\n",
argv[0], outfiles[i]);
exit(EXIT_FAILURE);
}
}
/* Get the list of input files either from the command line or
from a file, or report an error if both are specified.
Note that if -outfile is given then there is no output file name
left on argv after option parsing. */
nfiles = argc - 2;
if (Output_list != NULL) nfiles++;
if (filelist == NULL) {
infiles = &argv[1];
}
else if (nfiles <= 0) {
infiles = read_file_names(filelist, &nfiles);
if (infiles == NULL) {
(void) fprintf(stderr,
"Error reading in file names from file \"%s\"\n",
filelist);
exit(EXIT_FAILURE);
}
}
else {
(void) fprintf(stderr,
"Do not specify both -filelist and input file names\n");
exit(EXIT_FAILURE);
}
/* Make sure that we have something to process */
if (nfiles == 0) {
(void) fprintf(stderr, "No input files specified\n");
exit(EXIT_FAILURE);
}
/* Get the expression from the file if needed */
if ((expression == NULL) && (expr_file == NULL)) {
(void) fprintf(stderr,
"An expression must be specified on the command line\n");
exit(EXIT_FAILURE);
}
else if (expression == NULL) {
expression = read_expression_file(expr_file);
}
/* Parse expression argument */
if (debug) fprintf(stderr, "Feeding in expression %s\n", expression);
lex_init(expression);
if (debug) yydebug = 1; else yydebug = 0;
yyparse();
lex_finalize();
/* Optimize the expression tree */
root = optimize(root);
/* Setup the input vector from the input files */
A = new_vector();
for (i=0; i<nfiles; i++) {
if (debug) fprintf(stderr,"Getting file[%d] %s\n", i, argv[i+1]);
scalar = new_scalar(eval_width);
vector_append(A, scalar);
scalar_free(scalar);
}
/* Construct initial symbol table from the A vector. Since setting
a symbol makes a copy, we have to get a handle to that copy. */
rootsym = sym_enter_scope(NULL);
ident = new_ident("A");
sym_set_vector(eval_width, NULL, A, ident, rootsym);
vector_free(A);
A = sym_lookup_vector(ident, rootsym);
if (A==NULL) {
(void) fprintf(stderr, "Error initializing symbol table\n");
exit(EXIT_FAILURE);
}
vector_incr_ref(A);
/* Add output symbols to the table */
if (Output_list == NULL) {
Output_values = NULL;
}
else {
Output_values = malloc(Output_list_size * sizeof(*Output_values));
for (i=0; i < Output_list_size; i++) {
ident = ident_lookup(Output_list[i].symbol);
scalar = new_scalar(eval_width);
sym_set_scalar(eval_width, NULL, scalar, ident, rootsym);
scalar_free(scalar);
Output_values[i] = sym_lookup_scalar(ident, rootsym);
}
}
/* Set default copy_all_header according to number of input files */
if (copy_all_header == DEFAULT_BOOL)
copy_all_header = (nfiles == 1);
if (value_for_illegal_operations == DEFAULT_DBL) {
if (use_nan_for_illegal_values)
value_for_illegal_operations = INVALID_DATA;
else
value_for_illegal_operations = 0.0;
}
/* Do math */
loop_options = create_loop_options();
set_loop_verbose(loop_options, verbose);
set_loop_clobber(loop_options, clobber);
#if MINC2
set_loop_v2format(loop_options, minc2_format);
#endif /* MINC2 */
set_loop_datatype(loop_options, datatype, is_signed,
valid_range[0], valid_range[1]);
set_loop_copy_all_header(loop_options, copy_all_header);
/* only set buffer size if specified */
if(max_buffer_size_in_kb != 0){
set_loop_buffer_size(loop_options, (long) 1024 * max_buffer_size_in_kb);
}
set_loop_check_dim_info(loop_options, check_dim_info);
voxel_loop(nfiles, infiles, nout, outfiles, arg_string, loop_options,
do_math, NULL);
free_loop_options(loop_options);
/* Clean up */
vector_free(A);
sym_leave_scope(rootsym);
if (expr_file != NULL) free(expression);
free(outfiles);
if (Output_list != NULL) free(Output_list);
if (Output_values != NULL) free(Output_values);
exit(EXIT_SUCCESS);
}
int main(int argc, char *argv[])
{
char *infile, *outfile;
char *arg_string;
int inmincid;
int input_vector_length;
int ivalue;
Loop_Options *loop_options;
Program_Data program_data;
/* Save time stamp and args */
arg_string = time_stamp(argc, argv);
/* Get arguments */
if (ParseArgv(&argc, argv, argTable, 0) || (argc != 3)) {
(void) fprintf(stderr, "\nUsage: %s [options] <in.mnc> <out.mnc>\n",
argv[0]);
(void) fprintf(stderr, " %s -help\n\n",
argv[0]);
exit(EXIT_FAILURE);
}
infile = argv[1];
outfile = argv[2];
/* Check for conflicting options */
if ((conversion_type != CONV_DEFAULT) &&
(linear_coefficients.numvalues > 0)) {
(void) fprintf(stderr,
"Do not specify -linear with other conversion options\n");
exit(EXIT_FAILURE);
}
/* Set up conversion information */
if (conversion_type == CONV_DEFAULT) conversion_type = CONV_MAGNITUDE;
program_data.conversion_type = conversion_type;
program_data.num_coefficients = 0;
program_data.linear_coefficients = NULL;
/* Check for coefficients for linear combination */
if (linear_coefficients.numvalues > 0) {
conversion_type = CONV_LINEAR;
program_data.conversion_type = conversion_type;
program_data.num_coefficients = linear_coefficients.numvalues;
program_data.linear_coefficients =
malloc(linear_coefficients.numvalues *
sizeof(*program_data.linear_coefficients));
for (ivalue=0; ivalue < linear_coefficients.numvalues; ivalue++) {
program_data.linear_coefficients[ivalue] =
linear_coefficients.values[ivalue];
}
}
/* Open the input file and get the vector length */
inmincid = miopen(infile, NC_NOWRITE);
input_vector_length = get_vector_length(inmincid);
if (input_vector_length < 0) {
fprintf(stderr, str_wrong_dimension_order);
exit(EXIT_FAILURE);
}
if (input_vector_length < 1) input_vector_length = 1;
/* Check that this length is okay */
if ((conversion_type == CONV_GREY) &&
(input_vector_length != 3) && (input_vector_length > 1)) {
(void) fprintf(stderr, "Input file does not contain RGB data\n");
exit(EXIT_FAILURE);
}
if ((conversion_type == CONV_LINEAR) &&
(input_vector_length != program_data.num_coefficients) &&
(input_vector_length > 1)) {
(void) fprintf(stderr,
"Input vector length does not match number of linear coefficients\n");
exit(EXIT_FAILURE);
}
/* Set up looping options */
loop_options = create_loop_options();
set_loop_clobber(loop_options, clobber);
set_loop_verbose(loop_options, verbose);
#if MINC2
set_loop_v2format(loop_options, v2format);
#endif /* MINC2 */
set_loop_datatype(loop_options, datatype, is_signed,
valid_range[0], valid_range[1]);
set_loop_output_vector_size(loop_options, 1);
set_loop_buffer_size(loop_options, (long) buffer_size * 1024);
set_loop_first_input_mincid(loop_options, inmincid);
/* Do loop */
voxel_loop(1, &infile, 1, &outfile, arg_string, loop_options,
do_makescalar, (void *) &program_data);
/* Free stuff */
if (program_data.linear_coefficients != NULL) {
free(program_data.linear_coefficients);
}
if (linear_coefficients.values != NULL) {
free(linear_coefficients.values);
}
exit(EXIT_SUCCESS);
}
int main(int argc, char *argv[])
{
char *infile, *outfile;
char *arg_string;
Loop_Options *loop_options;
int inmincid;
Lookup_Data lookup_data;
/* Save time stamp and args */
arg_string = time_stamp(argc, argv);
/* Get arguments */
if (ParseArgv(&argc, argv, argTable, 0) || (argc != 3)) {
(void) fprintf(stderr, "\nUsage: %s [options] <in.mnc> <out.mnc>\n",
argv[0]);
(void) fprintf(stderr, " %s -help\n\n",
argv[0]);
exit(EXIT_FAILURE);
}
infile = argv[1];
outfile = argv[2];
/* Get the appropriate lookup table */
if ((lookup_file != NULL) || (lookup_string != NULL)) {
lookup_data.lookup_table = read_lookup_table(lookup_file, lookup_string);
}
else {
switch (lookup_type) {
case LU_GRAY:
lookup_data.lookup_table = &gray_lookup;
break;
case LU_HOTMETAL:
lookup_data.lookup_table = &hotmetal_lookup;
break;
case LU_SPECTRAL:
lookup_data.lookup_table = &spectral_lookup;
break;
case LU_TABLE:
break;
default:
fprintf(stderr, "Unknown lookup type: %d\n", lookup_type);
break;
}
}
/* Get the null value */
lookup_data.null_value =
get_null_value(lookup_data.lookup_table->vector_length,
null_value_string);
/* Open the input file and get the range */
inmincid = miopen(infile, NC_NOWRITE);
if (!discrete_lookup && (lookup_range[0] == DEFAULT_RANGE)) {
get_full_range(inmincid, lookup_range);
}
if (lookup_min != DEFAULT_RANGE)
lookup_range[0] = lookup_min;
if (lookup_max != DEFAULT_RANGE)
lookup_range[1] = lookup_max;
/* Set up lookup information */
lookup_data.invert = invert_table;
lookup_data.range[0] = lookup_range[0];
lookup_data.range[1] = lookup_range[1];
lookup_data.discrete = discrete_lookup;
/* Set up looping options */
loop_options = create_loop_options();
set_loop_clobber(loop_options, clobber);
set_loop_verbose(loop_options, verbose);
#if MINC2
set_loop_v2format(loop_options, minc2_format);
#endif /* MINC2 */
set_loop_datatype(loop_options, datatype, is_signed,
valid_range[0], valid_range[1]);
set_loop_convert_input_to_scalar(loop_options, TRUE);
set_loop_output_vector_size(loop_options,
lookup_data.lookup_table->vector_length);
set_loop_buffer_size(loop_options, (long) buffer_size * 1024);
set_loop_first_input_mincid(loop_options, inmincid);
/* Do loop */
voxel_loop(1, &infile, 1, &outfile, arg_string, loop_options,
do_lookup, (void *) &lookup_data);
/* Free stuff */
if (lookup_data.null_value != NULL) free(lookup_data.null_value);
if (lookup_data.lookup_table->free_data) {
free(lookup_data.lookup_table->table);
free(lookup_data.lookup_table);
}
exit(EXIT_SUCCESS);
}
int main(int argc, char *argv[])
{
char **infiles, *outfiles[3];
int nfiles, nout;
char *arg_string;
Norm_Data norm_data;
Average_Data average_data;
Loop_Options *loop_options;
double *vol_mean, vol_total, nvols, global_mean, total_weight;
int ifile, iweight;
int weights_specified;
int first_mincid, dimid, varid, dim[MAX_VAR_DIMS];
int ndims;
long start, count;
int old_ncopts;
int strlength;
char dimname[MAX_NC_NAME];
/* Save time stamp and args */
arg_string = time_stamp(argc, argv);
/* Get arguments */
if (ParseArgv(&argc, argv, argTable, 0) || (argc < 2)) {
(void) fprintf(stderr,
"\nUsage: %s [options] [<in1.mnc> ...] <out.mnc>\n",
argv[0]);
(void) fprintf(stderr,
" %s -help\n\n", argv[0]);
exit(EXIT_FAILURE);
}
outfiles[0] = outfiles[1] = outfiles[2] = NULL;
outfiles[0] = argv[argc-1];
nout = 1;
if( sdfile != NULL )
outfiles[nout++] = sdfile;
if( weightfile != NULL )
outfiles[nout++] = weightfile;
first_mincid = MI_ERROR;
/* Get the list of input files either from the command line or
from a file, or report an error if both are specified */
nfiles = argc - 2;
if (filelist == NULL) {
infiles = &argv[1];
}
else if (nfiles <= 0) {
infiles = read_file_names(filelist, &nfiles);
if (infiles == NULL) {
(void) fprintf(stderr,
"Error reading in file names from file \"%s\"\n",
filelist);
exit(EXIT_FAILURE);
}
}
else {
(void) fprintf(stderr,
"Do not specify both -filelist and input file names\n");
exit(EXIT_FAILURE);
}
/* Make sure that we have something to process */
if (nfiles == 0) {
(void) fprintf(stderr, "No input files specified\n");
exit(EXIT_FAILURE);
}
/* Set default value of copy_all_header */
if (copy_all_header == DEFAULT_BOOLEAN) {
copy_all_header = (nfiles <= 1);
}
/* Are we averaging over a dimension? */
average_data.averaging_over_dimension = (averaging_dimension != NULL);
/* Check for weights and width-weighting */
weights_specified = weights.numvalues > 0;
if (weights_specified && width_weighted) {
(void) fprintf(stderr,
"%s: Please do not specify weights and width-weighting.\n",
argv[0]);
exit(EXIT_FAILURE);
}
/* Default is no weighting */
average_data.num_weights = 0;
average_data.weights = NULL;
/* Check for weights */
if (weights_specified) {
if (averaging_dimension == NULL) {
if (weights.numvalues != nfiles) {
(void) fprintf(stderr,
"%s: Number of weights does not match number of files.\n",
argv[0]);
exit(EXIT_FAILURE);
}
}
else {
if (nfiles > 1) {
(void) fprintf(stderr,
"%s: Only one input file allowed with -weights and -avgdim.\n",
argv[0]);
exit(EXIT_FAILURE);
}
/* Check that the dimension size matches the number of weights */
first_mincid = miopen(infiles[0], NC_NOWRITE);
dimid = ncdimid(first_mincid, averaging_dimension);
(void) ncdiminq(first_mincid, dimid, NULL, &count);
if (weights.numvalues != count) {
(void) fprintf(stderr,
"%s: Number of weights does not match size of dimension.\n",
argv[0]);
}
}
/* Save the weights */
average_data.num_weights = weights.numvalues;
average_data.weights =
malloc(sizeof(*average_data.weights) * average_data.num_weights);
for (iweight=0; iweight < average_data.num_weights; iweight++) {
average_data.weights[iweight] = weights.values[iweight];
}
free(weights.values);
}
/* Check for width weighting */
if (width_weighted) {
/* Check for errors */
if (averaging_dimension == NULL) {
(void) fprintf(stderr,
"%s: Please specify -avgdim with -width_weighted.\n",
argv[0]);
exit(EXIT_FAILURE);
}
if (nfiles > 1) {
(void) fprintf(stderr,
"%s: Use -width_weighted with only one input file.\n",
argv[0]);
exit(EXIT_FAILURE);
}
/* Open the file */
first_mincid = miopen(infiles[0], NC_NOWRITE);
/* Get the dimension id */
dimid = ncdimid(first_mincid, averaging_dimension);
/* Look for the width variable */
strlength = MAX_NC_NAME - strlen(WIDTH_SUFFIX) - 1;
(void) strncpy(dimname, averaging_dimension, strlength);
dimname[strlength] = '\0';
(void) strcat(dimname, WIDTH_SUFFIX);
old_ncopts = ncopts; ncopts = 0;
varid = ncvarid(first_mincid, dimname);
(void) ncvarinq(first_mincid, varid, NULL, NULL, &ndims, dim, NULL);
ncopts = old_ncopts;
if (varid != MI_ERROR) {
/* Check that things match up */
if ((ndims != 1) || (dim[0] != dimid)) {
(void) fprintf(stderr,
"%s: Dimension width variable does not match avgdim.\n",
argv[0]);
}
/* Get the size of the dimension */
(void) ncdiminq(first_mincid, dim[0], NULL, &count);
average_data.num_weights = count;
average_data.weights =
malloc(sizeof(*average_data.weights) * average_data.num_weights);
/* Read in the widths */
start = 0;
(void) mivarget(first_mincid, varid, &start, &count, NC_DOUBLE, NULL,
average_data.weights);
}
} /* If width_weighted */
/* Check that weights sum to non-zero. We don't need to normalize them,
since a running sum is done in the averaging. */
if (average_data.num_weights > 0) {
total_weight = 0.0;
for (iweight=0; iweight < average_data.num_weights; iweight++) {
total_weight += average_data.weights[iweight];
}
if (total_weight == 0.0) {
(void) fprintf(stderr, "%s: Weights sum to zero.\n", argv[0]);
exit(EXIT_FAILURE);
}
}
/* If we don't have weights, each input will get a weight of 1 */
if (average_data.num_weights == 0)
total_weight = nfiles;
/* Check the cumulative weight thresholding */
if (weight_thresh > 0.0 && weight_thresh_fraction > 0.0){
(void) fprintf(stderr,
"Do not specify both -min_weight -min_weight_fraction\n");
exit(EXIT_FAILURE);
}
else if( weight_thresh_fraction > 0.0 ){
weight_thresh = weight_thresh_fraction * total_weight;
}
average_data.weight_thresh = weight_thresh;
/* Check for binarization */
if (binarize) {
if (normalize == TRUE) {
(void) fprintf(stderr,
"%s: Normalization and binarization cannot both be specified\n",
argv[0]);
exit(EXIT_FAILURE);
}
normalize = FALSE;
if (binvalue != -DBL_MAX) {
binrange[0] = binvalue - 0.5;
binrange[1] = binvalue + 0.5;
}
if (binrange[0] > binrange[1]) {
(void) fprintf(stderr,
"%s: Please specify a binarization range with min less than max\n",
argv[0]);
exit(EXIT_FAILURE);
}
average_data.binrange[0] = binrange[0];
average_data.binrange[1] = binrange[1];
}
average_data.binarize = binarize;
/* Store the ignore above/below values */
average_data.ignore_below = ignore_below;
average_data.ignore_above = ignore_above;
/* Check for no specification of normalization */
#ifdef NO_DEFAULT_NORM
if (normalize == -1) {
(void) fprintf(stderr, "\n%s: %s\n\n%s\n%s\n%s\n%s\n%s\n\n", argv[0],
"Please specify either -norm or -nonorm.",
"The default setting for normalization is being changed from \"-norm\" to",
"\"-nonorm\". To prevent undetected problems with data, this program will ",
"not work unless one of these flags is explicitly given on the command-line",
"(ie. no default is permitted). The new default will come into effect some",
"time in the future."
);
exit(EXIT_FAILURE);
}
#endif
/* Do normalization if needed */
average_data.norm_factor =
malloc(sizeof(*average_data.norm_factor) * nfiles);
if (normalize) {
vol_mean = malloc(sizeof(*vol_mean) * nfiles);
loop_options = create_loop_options();
set_loop_verbose(loop_options, FALSE);
#if MINC2
set_loop_v2format(loop_options, minc2_format);
#endif /* MINC2 */
set_loop_accumulate(loop_options, TRUE, 0, NULL, NULL);
set_loop_buffer_size(loop_options, (long) 1024 * max_buffer_size_in_kb);
set_loop_check_dim_info(loop_options, check_dimensions);
vol_total = 0.0;
nvols = 0;
if (verbose) {
(void) fprintf(stderr, "Normalizing:");
(void) fflush(stderr);
}
for (ifile=0; ifile < nfiles; ifile++) {
norm_data.threshold_set = FALSE;
norm_data.sum0 = 0.0;
norm_data.sum1 = 0.0;
if (verbose) {
(void) fprintf(stderr, ".");
(void) fflush(stderr);
}
if (first_mincid != MI_ERROR) {
set_loop_first_input_mincid(loop_options, first_mincid);
first_mincid = MI_ERROR;
}
voxel_loop(1, &infiles[ifile], 0, NULL, NULL, loop_options,
do_normalization, (void *) &norm_data);
if (norm_data.sum0 > 0.0) {
vol_mean[ifile] = norm_data.sum1 / norm_data.sum0;
vol_total += vol_mean[ifile];
nvols++;
}
else {
vol_mean[ifile] = 0.0;
}
if (debug) {
(void) fprintf(stderr, "Volume %d mean = %.15g\n",
ifile, vol_mean[ifile]);
}
}
free_loop_options(loop_options);
if (verbose) {
(void) fprintf(stderr, "Done\n");
(void) fflush(stderr);
}
if (nvols > 0)
global_mean = vol_total / nvols;
else
global_mean = 0.0;
for (ifile=0; ifile < nfiles; ifile++) {
if (vol_mean[ifile] > 0.0)
average_data.norm_factor[ifile] = global_mean / vol_mean[ifile];
else
average_data.norm_factor[ifile] = 0.0;
if (debug) {
(void) fprintf(stderr, "Volume %d norm factor = %.15g\n",
ifile, average_data.norm_factor[ifile]);
}
}
free(vol_mean);
}
else {
for (ifile=0; ifile < nfiles; ifile++) {
average_data.norm_factor[ifile] = 1.0;
}
}
/* Do averaging */
average_data.need_sd = (sdfile != NULL);
average_data.need_weight = (weightfile != NULL);
loop_options = create_loop_options();
if (first_mincid != MI_ERROR) {
set_loop_first_input_mincid(loop_options, first_mincid);
first_mincid = MI_ERROR;
}
set_loop_verbose(loop_options, verbose);
set_loop_clobber(loop_options, clobber);
set_loop_datatype(loop_options, datatype, is_signed,
valid_range[0], valid_range[1]);
set_loop_accumulate(loop_options, TRUE, 1, start_average, finish_average);
set_loop_copy_all_header(loop_options, copy_all_header);
set_loop_dimension(loop_options, averaging_dimension);
set_loop_buffer_size(loop_options, (long) 1024 * max_buffer_size_in_kb);
set_loop_check_dim_info(loop_options, check_dimensions);
voxel_loop(nfiles, infiles, nout, outfiles, arg_string, loop_options,
do_average, (void *) &average_data);
free_loop_options(loop_options);
/* Free stuff */
free(average_data.weights);
free(average_data.norm_factor);
exit(EXIT_SUCCESS);
}
