void read_data()
{
/* read from external file to internal table */
table_read("mydata","./workspace/eg03_mixednormal_fakedata.txt",1);
PAUSE
return;
}
void read_data()
{
/* read in a 1-column table from an external file, into an internal table called mydata */
/* change the second parameter when reading real data instead of fake data */
// TODO: change the third parameter to the actual number of columns!
table_read("mydata", "./workspace/mymodel_fakedata.txt", 0);
/* add columns for the likelihood function to write predictions */
// table_addcolumn("mydata", <column_name>);
// ...
PAUSE // examine printout to visually check the proper data was read
return;
}
void read_data()
{
/* read table from external file into internal file called 'mydata' */
table_read("mydata","./workspace/EgDataz2_seedrain.txt",4);
numdata = table_numrows("mydata");
/* in this case, we are going to write into our internal table, the model predictions */
/* so we need an extra columnd for that */
table_addcolumn("mydata","predlambda"); /* model predicted average seedling count */
table_addcolumn("mydata","simulatedcount"); /* model output: random draw for seedling count */
PAUSE
return;
}
cache_entry *
load_cache_table (char *file_name)
{
cache_entry *cache = NULL;
cache_entry **last = &cache;
table *file = table_open (file_name);
table_entry *entry;
while ((entry = table_read (file)) != NULL)
{
cache_entry *new_rule = ZALLOC (cache_entry);
new_rule->line = entry->line;
new_rule->entry_type = name2i (entry->field[ca_type], cache_type_map);
new_rule->name = entry->field[ca_derived_name];
filter_parse (&new_rule->original_fields, entry->field[ca_field_name]);
new_rule->type = entry->field[ca_type_def];
/* expression is the concatenation of the remaining fields */
if (entry->nr_fields > ca_expression)
{
int len = 0;
int chi;
for (chi = ca_expression; chi < entry->nr_fields; chi++)
{
len += strlen (" : ") + strlen (entry->field[chi]);
}
new_rule->expression = NZALLOC (char, len);
strcpy (new_rule->expression, entry->field[ca_expression]);
for (chi = ca_expression + 1; chi < entry->nr_fields; chi++)
{
strcat (new_rule->expression, " : ");
strcat (new_rule->expression, entry->field[chi]);
}
}
/* insert it */
*last = new_rule;
last = &new_rule->next;
}
/**
* read FITS file and fill 'IMAGE' structure (with headers and tables)
* can't work with image stack - opens the first image met
* works only with binary tables
*/
IMAGE* readFITS(char *filename, IMAGE **fits){
FNAME();
#define TRYRET(f, ...) do{TRYFITS(f, __VA_ARGS__); if(fitsstatus) goto returning;}while(0)
fitsfile *fp;
int i, j, hdunum = 0, hdutype, nkeys, keypos;
int naxis;
long naxes[2];
char card[FLEN_CARD];
IMAGE *img = MALLOC(IMAGE, 1);
TRYRET(fits_open_file, &fp, filename, READONLY);
FITSFUN(fits_get_num_hdus, fp, &hdunum);
if(hdunum < 1){
WARNX(_("Can't read HDU"));
fitsstatus = 1;
goto returning;
}
// get image dimensions
TRYRET(fits_get_img_param, fp, 2, &img->dtype, &naxis, naxes);
if(naxis > 2){
WARNX(_("Images with > 2 dimensions are not supported"));
fitsstatus = 1;
goto returning;
}
img->width = naxes[0];
img->height = naxes[1];
DBG("got image %ldx%ld pix, bitpix=%d", naxes[0], naxes[1], img->dtype);
// loop through all HDUs
KeyList *list = img->keylist;
int imghdu = -1;
for(i = 1; !(fits_movabs_hdu(fp, i, &hdutype, &fitsstatus)); ++i){
int hdutype;
TRYFITS(fits_get_hdu_type, fp, &hdutype);
// types: IMAGE_HDU , ASCII_TBL, BINARY_TBL
if(fitsstatus) continue;
DBG("HDU type %d", hdutype);
//if(hdutype == ASCII_TBL || hdutype == BINARY_TBL){
if(hdutype == BINARY_TBL){
table_read(img, fp);
continue;
}
if(imghdu < 1) imghdu = i;
TRYFITS(fits_get_hdrpos, fp, &nkeys, &keypos);
if(fitsstatus) continue;
//DBG("HDU # %d of %d keys", i, nkeys);
for(j = 1; j <= nkeys; ++j){
FITSFUN(fits_read_record, fp, j, card);
if(!fitsstatus){
if(!list_add_record(&list, card)){
/// "Не могу добавить запись в список"
WARNX(_("Can't add record to list"));
}
//DBG("key %d: %s", j, card);
}
}
}
img->keylist = list;
if(fitsstatus == END_OF_FILE){
fitsstatus = 0;
}else{
fits_report_error(stderr, fitsstatus);
goto returning;
}
if(fits_movabs_hdu(fp, imghdu, &hdutype, &fitsstatus)){
WARNX(_("Can't open image HDU #%d"), imghdu);
fitsstatus = 1;
goto returning;
}
size_t sz = naxes[0] * naxes[1];
img->data = MALLOC(double, sz);
int stat = 0;
TRYFITS(fits_read_img, fp, TDOUBLE, 1, sz, NULL, img->data, &stat);
if(stat) WARNX(_("Found %d pixels with undefined value"), stat);
DBG("ready");
#undef TRYRET
returning:
if(fitsstatus){
imfree(&img);
}
FITSFUN(fits_close_file, fp);
if(fits){
FREE(*fits);
*fits = img;
}
return img;
}
/*
* perform some basic tests
*/
static void io_test(table_t *tab_p)
{
int ret, bucket_n, entry_n;
table_t *tab2_p;
(void)printf("Performing I/O tests:\n");
(void)fflush(stdout);
#if 0
{
long key, data;
(void)table_clear(tab_p);
key = 1;
data = 2;
(void)table_insert(tab_p, &key, sizeof(key), &data, sizeof(data), NULL, 0);
key = 3;
data = 4;
(void)table_insert(tab_p, &key, sizeof(key), &data, sizeof(data), NULL, 0);
key = 5;
data = 6;
(void)table_insert(tab_p, &key, sizeof(key), &data, sizeof(data), NULL, 0);
(void)table_adjust(tab_p, 0);
dump_table(tab_p);
}
#endif
ret = table_info(tab_p, &bucket_n, &entry_n);
if (ret != TABLE_ERROR_NONE) {
(void)fprintf(stderr, "could not get info of table: %s\n",
table_strerror(ret));
exit(1);
}
(void)printf("Table we are writing has %d buckets and %d entries\n",
bucket_n, entry_n);
/*
* dump the table to disk
*/
int pmode = 0640;
#ifdef win32
pmode = _S_IREAD | _S_IWRITE;
#endif
(void)unlink(TABLE_FILE);
ret = table_write(tab_p, TABLE_FILE, pmode);
if (ret != TABLE_ERROR_NONE) {
(void)fprintf(stderr, "could not write table to '%s': %s\n",
TABLE_FILE, table_strerror(ret));
exit(1);
}
#if 0
dump_table(tab_p);
#endif
/*
* now read back in the table
*/
tab2_p = table_read(TABLE_FILE, &ret);
if (tab2_p == NULL) {
(void)fprintf(stderr, "could not read in file '%s': %s\n",
TABLE_FILE, table_strerror(ret));
exit(1);
}
(void)printf("Testing table-read...\n");
if (test_eq(tab_p, tab2_p, 0)) {
(void)printf(" equal.\n");
}
else {
(void)printf(" NOT equal.\n");
}
ret = table_free(tab2_p);
if (ret != TABLE_ERROR_NONE) {
(void)fprintf(stderr, "could not free read table: %s\n",
table_strerror(ret));
exit(1);
}
/*
* mmap in the table
*/
tab2_p = table_mmap(TABLE_FILE, &ret);
if (tab2_p == NULL) {
(void)fprintf(stderr, "could not mmap file '%s': %s\n",
TABLE_FILE, table_strerror(ret));
exit(1);
}
(void)printf("Testing table-mmap...\n");
if (test_eq(tab2_p, tab_p, 0)) {
(void)printf(" equal.\n");
}
else {
(void)printf(" NOT equal.\n");
}
ret = table_munmap(tab2_p);
if (ret != TABLE_ERROR_NONE) {
(void)fprintf(stderr, "could not munmap file '%s': %s\n",
TABLE_FILE, table_strerror(ret));
exit(1);
}
}