/* Note: this file has been modified from its original form by the Astrometry.net team. For details see http://astrometry.net */ /* $Id: qfits_table.c,v 1.20 2007/01/10 12:24:45 yjung Exp $ * * This file is part of the ESO QFITS Library * Copyright (C) 2001-2004 European Southern Observatory * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */ /* * $Author: yjung $ * $Date: 2007/01/10 12:24:45 $ * $Revision: 1.20 $ * $Name: qfits-6_2_0 $ */ /*----------------------------------------------------------------------------- Includes -----------------------------------------------------------------------------*/ #include #include #include #include #include #include #include #include #include "qfits_config.h" #include "qfits_table.h" #include "qfits_float.h" #include "qfits_std.h" #include "qfits_byteswap.h" #include "qfits_tools.h" #include "qfits_time.h" #include "qfits_rw.h" #include "qfits_md5.h" #include "qfits_error.h" #include "qfits_memory.h" /*----------------------------------------------------------------------------- Define -----------------------------------------------------------------------------*/ #define ELEMENT_MAX_DISPLAY_SIZE 50 /*----------------------------------------------------------------------------- Function prototypes -----------------------------------------------------------------------------*/ static char * qfits_bintable_field_to_string(const qfits_table *, int, int,int); static char * qfits_asciitable_field_to_string(const qfits_table *, int, int, int); static char * qfits_build_format(const qfits_col *); static int qfits_table_append_bin_xtension(FILE *, const qfits_table *, const void **); static int qfits_table_append_ascii_xtension(FILE *, const qfits_table *, const void **); static int qfits_table_append_data(FILE *, const qfits_table *, const void **); static int qfits_table_get_field_size(int, const qfits_col *); static char * qfits_strstrip(const char *); static double qfits_str2dec(const char *, int); /*----------------------------------------------------------------------------*/ /** * @defgroup qfits_table FITS table handling * */ /*----------------------------------------------------------------------------*/ /**@{*/ /*----------------------------------------------------------------------------- Function codes -----------------------------------------------------------------------------*/ const qfits_col* qfits_table_get_col(const qfits_table* t, int i) { return t->col + i; } qfits_table* qfits_table_copy(const qfits_table* t) { qfits_table* dest = calloc(1, sizeof(qfits_table)); assert(dest); memcpy(dest, t, sizeof(qfits_table)); dest->col = calloc(dest->nc, sizeof(qfits_col)); memcpy(dest->col, t->col, dest->nc * sizeof(qfits_col)); return dest; } int qfits_is_table_header(const qfits_header* hdr) { char* value; int ttype; char buf[FITS_LINESZ + 1]; ttype = QFITS_INVALIDTABLE; value = qfits_header_getstr(hdr, "XTENSION"); if (!value) return ttype; qfits_pretty_string_r(value, buf); value = buf; if (!strcmp(value, "TABLE")) { ttype = QFITS_ASCIITABLE; } else if (!strcmp(value, "BINTABLE")) { ttype = QFITS_BINTABLE; } return ttype; } /*----------------------------------------------------------------------------*/ /** @brief Generate a default primary header to store tables @return the header object */ /*----------------------------------------------------------------------------*/ qfits_header * qfits_table_prim_header_default(void) { qfits_header * fh; fh = qfits_header_new(); qfits_header_append(fh, "SIMPLE", "T", "Standard FITS file", NULL); qfits_header_append(fh, "BITPIX", "8", "ASCII or bytes array", NULL); qfits_header_append(fh, "NAXIS", "0", "Minimal header", NULL); qfits_header_append(fh, "EXTEND", "T", "There may be FITS ext", NULL); qfits_header_append(fh, "END", NULL, NULL, NULL); return fh; } /*----------------------------------------------------------------------------*/ /** @brief Generate a default extension header to store tables @return the header object */ /*----------------------------------------------------------------------------*/ qfits_header * qfits_table_ext_header_default(const qfits_table * t) { qfits_header * fh; qfits_col * curr_col; char str_val[FITS_LINESZ]; char str_val2[FITS_LINESZ]; char * date; int tab_width; int col_pos; int i; /* Compute the table width */ if ((tab_width = qfits_compute_table_width(t)) == -1) { qfits_error("cannot get the table width"); return NULL; } /* Create fits header */ if ((fh=qfits_header_new()) == NULL) { qfits_error("cannot create new fits header"); return NULL; } /* Check the kind of table */ if (t->tab_t == QFITS_BINTABLE) { /* Write extension header */ qfits_header_append(fh, "XTENSION", "BINTABLE", "FITS Binary Table Extension", NULL); qfits_header_append(fh, "BITPIX", "8", "8-bits character format", NULL); qfits_header_append(fh, "NAXIS", "2","Tables are 2-D char. array",NULL); sprintf(str_val, "%d", tab_width); qfits_header_append(fh, "NAXIS1", str_val, "Bytes in row", NULL); sprintf(str_val, "%d", (int)(t->nr)); qfits_header_append(fh, "NAXIS2", str_val, "No. of rows in table",NULL); qfits_header_append(fh, "PCOUNT", "0", "Parameter count always 0",NULL); qfits_header_append(fh, "GCOUNT", "1", "Group count always 1", NULL); sprintf(str_val, "%d", (int)(t->nc)); qfits_header_append(fh, "TFIELDS", str_val, "No. of col in table",NULL); /* Columns descriptors */ curr_col = t->col; for (i=0; inc; i++) { sprintf(str_val, "TFORM%d", i+1); sprintf(str_val2, "'%s'", qfits_build_format(curr_col)); qfits_header_append(fh, str_val, str_val2, "Format of field", NULL); sprintf(str_val, "TTYPE%d", i+1); sprintf(str_val2, "%s", curr_col->tlabel); qfits_header_append(fh, str_val, str_val2, "Field label", NULL); if (strlen(curr_col->tunit)) { sprintf(str_val, "TUNIT%d", i+1); sprintf(str_val2, "%s", curr_col->tunit); //printf("Setting '%s' = '%s'\n", str_val, str_val2); qfits_header_append(fh, str_val, str_val2, "Physical unit of field", NULL); } if (curr_col->zero_present) { sprintf(str_val, "TZERO%d", i+1); sprintf(str_val2, "%f", curr_col->zero); qfits_header_append(fh, str_val, str_val2, "NULL value is defined", NULL); } if (curr_col->scale_present) { sprintf(str_val, "TSCAL%d", i+1); sprintf(str_val2, "%f", curr_col->scale); qfits_header_append(fh, str_val, str_val2, "Scaling applied", NULL); } curr_col++; } qfits_header_append(fh,"ORIGIN","ESO-QFITS", "Written by QFITS", NULL); date = qfits_get_datetime_iso8601(); sprintf(str_val, "'%s'", date); qfits_header_append(fh, "DATE", str_val, "[UTC] Date of writing", NULL); qfits_header_append(fh, "END", NULL, NULL, NULL); } else if (t->tab_t == QFITS_ASCIITABLE) { /* Write extension header */ qfits_header_append(fh, "XTENSION", "TABLE", "FITS ASCII Table Extension", NULL); qfits_header_append(fh, "BITPIX", "8", "8-bits character format", NULL); qfits_header_append(fh, "NAXIS", "2", "ASCII table has 2 axes", NULL); /* Fill the header */ sprintf(str_val, "%d", tab_width); qfits_header_append(fh, "NAXIS1", str_val, "Characters in a row", NULL); sprintf(str_val, "%d", (int)(t->nr)); qfits_header_append(fh, "NAXIS2", str_val, "No. of rows in table",NULL); qfits_header_append(fh, "PCOUNT", "0", "No group parameters", NULL); qfits_header_append(fh, "GCOUNT", "1", "Only one group", NULL); sprintf(str_val, "%d", (int)(t->nc)); qfits_header_append(fh, "TFIELDS", str_val, "No. of col in table",NULL); qfits_header_append(fh, "ORIGIN","ESO-QFITS","Written by QFITS",NULL); date = qfits_get_datetime_iso8601(); sprintf(str_val, "'%s'", date); qfits_header_append(fh, "DATE", str_val, "[UTC] Date of writing", NULL); /* Columns descriptors */ curr_col = t->col; col_pos = 1; for (i=0; inc; i++) { sprintf(str_val, "TTYPE%d", i+1); sprintf(str_val2, "%s", curr_col->tlabel); qfits_header_append(fh, str_val, str_val2, "Field label", NULL); sprintf(str_val, "TFORM%d", i+1); sprintf(str_val2, "'%s'", qfits_build_format(curr_col)); qfits_header_append(fh, str_val, str_val2, "Format of field", NULL); sprintf(str_val, "TBCOL%d", i+1); sprintf(str_val2, "%d", col_pos); qfits_header_append(fh, str_val, str_val2,"Start column of field", NULL); col_pos += curr_col->atom_nb; sprintf(str_val, "TUNIT%d", i+1); sprintf(str_val2, "%s", curr_col->tunit); qfits_header_append(fh, str_val, str_val2, "Physical unit of field", NULL); if (curr_col->zero_present) { sprintf(str_val, "TZERO%d", i+1); sprintf(str_val2, "%f", curr_col->zero); qfits_header_append(fh, str_val, str_val2, "NULL value is defined", NULL); } if (curr_col->scale_present) { sprintf(str_val, "TSCAL%d", i+1); sprintf(str_val2, "%f", curr_col->scale); qfits_header_append(fh, str_val, str_val2, "Scaling applied", NULL); } curr_col++; } qfits_header_append(fh, "END", NULL, NULL, NULL); } else { qfits_error("Table type not known"); qfits_header_destroy(fh); return NULL; } return fh; } /*----------------------------------------------------------------------------*/ /** @brief Table object constructor @param filename Name of the FITS file associated to the table @param table_type Type of the table (QFITS_ASCIITABLE or QFITS_BINTABLE) @param table_width Width in bytes of the table @param nb_cols Number of columns @param nb_raws Number of raws @return The table object The columns are also allocated. The object has to be deallocated with qfits_table_close() */ /*----------------------------------------------------------------------------*/ qfits_table * qfits_table_new( const char * filename, int table_type, int table_width, int nb_cols, int nb_raws) { qfits_table * qt; qt = qfits_malloc(sizeof(qfits_table)); strcpy(qt->filename, filename); qt->tab_t = table_type; qt->nc = nb_cols; qt->nr = nb_raws; if (qt->nc) qt->col = qfits_calloc(qt->nc, sizeof(qfits_col)); else qt->col = NULL; qt->tab_w = table_width; return qt; } /*----------------------------------------------------------------------------*/ /** @brief Fill a column object with some provided informations @param qc Pointer to the column that has to be filled @param unit Unit of the data @param label Label of the column @param disp Way to display the data @param nullval Null value @param atom_nb Number of atoms per field. According to the type, an atom is a double, an int, a char, ... @param atom_dec_nb Number of decimals as specified in TFORM @param atom_size Size in bytes of the field for ASCII tables, and of an atom for BIN tables. ASCII tables only contain 1 atom per field (except for A type where you can of course have more than one char per field) @param atom_type Type of data (11 types for BIN, 5 for ASCII) @param zero_present Flag to use or not zero @param zero Zero value @param scale_present Flag to use or not scale @param scale Scale value @param offset_beg Gives the position of the column @return -1 in error case, 0 otherwise */ /*----------------------------------------------------------------------------*/ int qfits_col_fill( qfits_col * qc, int atom_nb, int atom_dec_nb, int atom_size, tfits_type atom_type, const char * label, const char * unit, const char * nullval, const char * disp, int zero_present, float zero, int scale_present, float scale, int offset_beg) { /* Number of atoms per column */ qc->atom_nb = atom_nb; /* Number of decimals in a field in ASCII table (0 in BINTABLE) */ qc->atom_dec_nb = atom_dec_nb; /* Size in bytes of an atom */ qc->atom_size = atom_size; /* Data type in the column */ qc->atom_type = atom_type; /* Label of the column */ strcpy(qc->tlabel, label); /* Unit of the column data */ strcpy(qc->tunit, unit); /* Null value*/ strcpy(qc->nullval, nullval); /* How to display the data */ strcpy(qc->tdisp, disp); /* Default values for zero and scales */ qc->zero_present = zero_present; qc->scale_present = scale_present; qc->zero = zero; qc->scale = scale; /* Number of bytes between two consecutive fields of the same column */ qc->off_beg = offset_beg; /* A column is a priori readable */ qc->readable = 1; return 0; } /* Creates a qfits_table* from the given qfits_header. Also requires the offset to the beginning of the data unit, and its size. (eg, via qfits_get_datinfo) The "filename" and "xtnum" args are purely for printing error messages. (the filename is copied to the qfits_table object, though) */ qfits_table * qfits_table_open2(const qfits_header* hdr, off_t offset_beg, size_t data_size, const char* filename, int xtnum) { qfits_table * tload; qfits_col * curr_col; char str_val[FITS_LINESZ+1]; char keyword[FITSVALSZ]; /* Table infos */ int table_type; int nb_col; int table_width; int nb_rows; /* Column infos */ char label[FITSVALSZ]; char unit[FITSVALSZ]; char disp[FITSVALSZ]; char nullval[FITSVALSZ]; int atom_nb; int atom_dec_nb; int atom_size; tfits_type atom_type; size_t theory_size; int zero_present; int scale_present; float zero; float scale; /* For ASCII tables */ int col_pos; int next_col_pos; /* For X type */ int nb_bits; int i; /* Identify a table and get the table type : ASCII or BIN */ if ((table_type = qfits_is_table_header(hdr)) == QFITS_INVALIDTABLE) { qfits_error("[%s] extension %d is not a table", filename, xtnum); return NULL; } /* Get number of columns and allocate them: nc <-> TFIELDS */ nb_col = qfits_header_getint(hdr, "TFIELDS", -1); if (nb_col == -1) { qfits_error("cannot read TFIELDS in [%s]:[%d]", filename, xtnum); return NULL; } /* Get the width in bytes of the table */ table_width = qfits_header_getint(hdr, "NAXIS1", -1); if (table_width == -1) { qfits_error("cannot read NAXIS1 in [%s]:[%d]", filename, xtnum); return NULL; } /* Get the number of rows */ nb_rows = qfits_header_getint(hdr, "NAXIS2", -1); if (nb_rows == -1) { qfits_error("cannot read NAXIS2 in [%s]:[%d]", filename, xtnum); return NULL; } /* Create the table object */ tload = qfits_table_new(filename, table_type, table_width, nb_col, nb_rows); /* Loop on all columns and get column descriptions */ curr_col = tload->col; for (i=0; inc; i++) { const char* nil = ""; /* label <-> TTYPE */ sprintf(keyword, "TTYPE%d", i+1); qfits_header_getstr_pretty(hdr, keyword, label, nil); /* unit <-> TUNIT */ sprintf(keyword, "TUNIT%d", i+1); qfits_header_getstr_pretty(hdr, keyword, unit, nil); /* disp <-> TDISP */ sprintf(keyword, "TDISP%d", i+1); qfits_header_getstr_pretty(hdr, keyword, disp, nil); /* nullval <-> TNULL */ sprintf(keyword, "TNULL%d", i+1); qfits_header_getstr_pretty(hdr, keyword, nullval, nil); /* atom_size, atom_nb, atom_dec_nb, atom_type <-> TFORM */ sprintf(keyword, "TFORM%d", i+1); if (qfits_header_getstr_pretty(hdr, keyword, str_val, NULL)) { qfits_error("cannot read [%s] in [%s]:[%d]", keyword, filename, xtnum); qfits_table_close(tload); return NULL; } /* Interpret the type in header */ if (qfits_table_interpret_type(str_val, &atom_nb, &atom_dec_nb, &atom_type, table_type) == -1) { qfits_error("cannot interpret column type: %s", str_val); qfits_table_close(tload); return NULL; } /* Set atom_size */ switch (atom_type) { case TFITS_BIN_TYPE_A: case TFITS_BIN_TYPE_L: case TFITS_BIN_TYPE_B: atom_size = 1; break; case TFITS_BIN_TYPE_I: atom_size = 2; break; case TFITS_BIN_TYPE_J: case TFITS_BIN_TYPE_E: case TFITS_ASCII_TYPE_I: case TFITS_ASCII_TYPE_E: case TFITS_ASCII_TYPE_F: atom_size = 4; break; case TFITS_BIN_TYPE_C: case TFITS_BIN_TYPE_P: atom_size = 4; atom_nb *= 2; break; case TFITS_BIN_TYPE_K: case TFITS_BIN_TYPE_D: case TFITS_ASCII_TYPE_D: atom_size = 8; break; case TFITS_BIN_TYPE_M: atom_size = 8; atom_nb *= 2; break; case TFITS_BIN_TYPE_X: atom_size = 1; nb_bits = atom_nb; atom_nb = (int)((nb_bits - 1)/ 8) + 1; break; case TFITS_ASCII_TYPE_A: atom_size = atom_nb; break; default: qfits_error("unrecognized type"); qfits_table_close(tload); return NULL; break; } /* zero <-> TZERO */ sprintf(keyword, "TZERO%d", i+1); zero_present = 1; zero = qfits_header_getdouble(hdr, keyword, HUGE_VAL); if (zero == HUGE_VAL) { zero = 0.0; zero_present = 0; } /* scale <-> TSCAL */ sprintf(keyword, "TSCAL%d", i+1); scale_present = 1; scale = qfits_header_getdouble(hdr, keyword, HUGE_VAL); if (scale == HUGE_VAL) { scale = 1.0; scale_present = 0; } /* Fill the current column object */ qfits_col_fill(curr_col, atom_nb, atom_dec_nb, atom_size, atom_type, label, unit, nullval, disp, zero_present, zero, scale_present, scale, offset_beg); /* Compute offset_beg but for the last column */ if (i < tload->nc - 1) { if (table_type == QFITS_ASCIITABLE) { /* column width <-> TBCOLi and TBCOLi+1 */ sprintf(keyword, "TBCOL%d", i+1); col_pos = qfits_header_getint(hdr, keyword, -1); if (col_pos == -1) { qfits_error("cannot read [%s] in [%s]", keyword, filename); qfits_table_close(tload); return NULL; } sprintf(keyword, "TBCOL%d", i+2); next_col_pos = qfits_header_getint(hdr, keyword, -1); if (next_col_pos == -1) { qfits_error("cannot read [%s] in [%s]", keyword, filename); qfits_table_close(tload); return NULL; } offset_beg += (int)(next_col_pos - col_pos); } else if (table_type == QFITS_BINTABLE) { offset_beg += atom_nb * atom_size; } } curr_col++; } /* Check that the theoretical data size is not far from the measured */ /* one by more than 2880 */ theory_size = (size_t)qfits_compute_table_width(tload) * (size_t)tload->nr; if (data_size < theory_size) { qfits_error("Inconsistent data sizes: found %i, expected %i.", data_size, theory_size); qfits_table_close(tload); return NULL; } /* Return */ return tload; } /*----------------------------------------------------------------------------*/ /** @brief Free a FITS table and associated pointers @param t qfits_table to free @return void Frees all memory associated to a qfits_table structure. */ /*----------------------------------------------------------------------------*/ void qfits_table_close(qfits_table * t) { if (t==NULL) return; if (t->nc>0) if (t->col!=NULL) qfits_free(t->col); qfits_free(t); return; } /*----------------------------------------------------------------------------*/ /** @brief Extract data from a column in a FITS table @param th Allocated qfits_table @param colnum Number of the column to extract (from 0 to colnum-1) @param selection boolean array to define the selected rows @return unsigned char array If selection is NULL, select the complete column. Extract a column from a FITS table and return the data as a bytes array. The returned array type and size are determined by the column object in the qfits_table and by the selection parameter. Returned array size in bytes is: nbselected * col->natoms * col->atom_size Numeric types are correctly understood and byte-swapped if needed, to be converted to the local machine type. NULL values have to be handled by the caller. The returned object must be deallocated with qfits_free(). */ /*----------------------------------------------------------------------------*/ unsigned char * qfits_query_column( const qfits_table * th, int colnum, const int * selection) { char * start; qfits_col * col; int field_size; unsigned char * array; unsigned char * r; unsigned char * inbuf; int table_width; int nb_rows; size_t size; int i; if (th->tab_w == -1) { /* Compute the table width in bytes */ if ((table_width = qfits_compute_table_width(th)) == -1) { qfits_error("cannot compute the table width"); return NULL; } } else table_width = th->tab_w; /* Compute the number of selected rows */ nb_rows = 0; if (selection == NULL) { nb_rows = th->nr; } else { for (i=0; inr; i++) if (selection[i] == 1) nb_rows++; } /* Pointer to requested column */ col = th->col + colnum; /* Test if column is empty */ if (nb_rows * col->atom_size * col->atom_nb == 0) col->readable = 0; /* Test if column is readable */ if (col->readable == 0) return NULL; /* Compute the size in bytes of one field stored in the file */ if ((field_size=qfits_table_get_field_size(th->tab_t,col))==-1) return NULL; /* Load input file */ if ((start=qfits_falloc((char *)(th->filename), 0, &size))==NULL) { qfits_error("cannot open table for query [%s]", th->filename); return NULL; } /* Allocate data array */ array = qfits_malloc(nb_rows * field_size * sizeof(char)); /* Position the input pointer at the begining of the column data */ r = array; inbuf = (unsigned char*)start + col->off_beg; /* Copy the values in array */ if (selection == NULL) { /* No selection : get the complete column */ for (i=0; inr; i++) { /* Copy all atoms on this field into array */ memcpy(r, inbuf, field_size); r += field_size; /* Jump to next line */ inbuf += table_width; } } else { /* Get only the selected rows */ for (i=0; inr; i++) { if (selection[i] == 1) { /* Copy all atoms on this field into array */ memcpy(r, inbuf, field_size); r += field_size; } /* Jump to next line */ inbuf += table_width; } } qfits_fdealloc(start, 0, size); /* SWAP the bytes if necessary */ #ifndef WORDS_BIGENDIAN if ((th->tab_t == QFITS_BINTABLE) && (col->atom_size > 1)) { r = array; for (i=0; iatom_nb; i++) { qfits_swap_bytes(r, col->atom_size); r += col->atom_size; } } #endif /* Return allocated and converted array */ return array; } /*----------------------------------------------------------------------------*/ /** @brief Extract consequtive values from a column in a FITS table @param th Allocated qfits_table @param colnum Number of the column to extract (from 0 to colnum-1) @param start_ind Index of the first row (0 for the first) @param nb_rows Number of rows to extract @return unsigned char array Does the same as qfits_query_column() but on a consequtive sequence of rows Spares the overhead of the selection object allocation The returned object must be deallocated with qfits_free(). */ /*----------------------------------------------------------------------------*/ unsigned char * qfits_query_column_seq( const qfits_table * th, int colnum, int start_ind, int nb_rows) { char * start; qfits_col * col; int field_size; unsigned char * array; unsigned char * r; unsigned char * inbuf; int table_width; size_t size; int i; if (th->tab_w == -1) { /* Compute the table width in bytes */ if ((table_width = qfits_compute_table_width(th)) == -1) { qfits_error("cannot compute the table width"); return NULL; } } else table_width = th->tab_w; /* Check the validity of start_ind and nb_rows */ if ((start_ind<0) || (start_ind+nb_rows>th->nr)) { qfits_error("bad start index and number of rows"); return NULL; } /* Pointer to requested column */ col = th->col + colnum; /* Test if column is empty */ if (nb_rows * col->atom_size * col->atom_nb == 0) col->readable = 0; /* Test if column is readable */ if (col->readable == 0) return NULL; /* Compute the size in bytes of one field stored in the file */ if ((field_size=qfits_table_get_field_size(th->tab_t,col))==-1) return NULL; /* Load input file */ if ((start=qfits_falloc((char *)(th->filename), 0, &size))==NULL) { qfits_error("cannot open table for query [%s]", th->filename); return NULL; } /* Allocate data array */ array = qfits_malloc(nb_rows * field_size * sizeof(char)); /* Position the input pointer at the begining of the column data */ r = array; inbuf = (unsigned char*)start + col->off_beg + table_width * start_ind; /* Copy the values in array */ /* Get only the selected rows */ for (i=0; itab_t == QFITS_BINTABLE) && (col->atom_size > 1)) { r = array; for (i=0; iatom_nb; i++) { qfits_swap_bytes(r, col->atom_size); r += col->atom_size; } } #endif /* Return allocated and converted array */ return array; } static int qfits_query_column_seq_to_array_endian( const qfits_table * th, int colnum, int start_ind, const int* indices, int nb_rows, unsigned char* destination, int dest_stride, int swap_endian) { qfits_col * col; int field_size; unsigned char * r; unsigned char * inbuf; int table_width; int i; int do_swap; int maxind; char* freeaddr; size_t freesize; size_t mapoffset; size_t maplen; if (th->tab_w == -1) { /* Compute the table width in bytes */ if ((table_width = qfits_compute_table_width(th)) == -1) { qfits_error("cannot compute the table width"); return -1; } } else table_width = th->tab_w; /* Check the validity of start_ind and nb_rows */ if ((start_ind<0) || (start_ind+nb_rows>th->nr)) { qfits_error("bad start index and number of rows"); return -1; } /* Pointer to requested column */ col = th->col + colnum; /* Test if column is empty */ if (nb_rows * col->atom_size * col->atom_nb == 0) col->readable = 0; /* Test if column is readable */ if (col->readable == 0) return -1; /* Compute the size in bytes of one field stored in the file */ if ((field_size=qfits_table_get_field_size(th->tab_t,col))==-1) return -1; /* Load input file */ if (indices) { maxind = 0; for (i=0; i 2GB files! mapoffset = col->off_beg + (size_t)table_width * (size_t)start_ind; // NOTE that this *isn't* (table_width * N) -- that can lead to trying to map // beyond the end of the file! maplen = (size_t)maxind * (size_t)table_width + (size_t)field_size; //printf("opening %s: %zu + %zu (column offset = %i, width=%i, start_index=%i)\n", th->filename, mapoffset, maplen, col->off_beg, table_width, start_ind); if ((inbuf = qfits_falloc2(th->filename, mapoffset, maplen, &freeaddr, &freesize)) == NULL) { qfits_error("cannot open table for reading column data [%s]", th->filename); return -1; } /* if ((start=qfits_falloc(th->filename, 0, &size))==NULL) { qfits_error("cannot open table for query [%s]", th->filename); return -1; } inbuf = (unsigned char*)start + col->off_beg + table_width * start_ind; */ /* Position the input pointer at the begining of the column data */ r = destination; do_swap = 0; #ifndef WORDS_BIGENDIAN if (swap_endian) if ((th->tab_t == QFITS_BINTABLE) && (col->atom_size > 1)) do_swap = 1; #endif /* Copy the values in array */ /* Get only the selected rows */ for (i=0; iatom_nb; j++) { qfits_swap_bytes(r2, col->atom_size); r2 += col->atom_size; } } #endif r += dest_stride; } //qfits_fdealloc(start, 0, size); qfits_fdealloc2(freeaddr, freesize); return 0; } int qfits_query_column_seq_to_array( const qfits_table * th, int colnum, int start_ind, int nb_rows, unsigned char* destination, int dest_stride) { return qfits_query_column_seq_to_array_endian(th, colnum, start_ind, NULL, nb_rows, destination, dest_stride, 1); } int qfits_query_column_seq_to_array_inds(const qfits_table * th, int colnum, const int* indices, int Ninds, unsigned char* destination, int dest_stride) { return qfits_query_column_seq_to_array_endian(th, colnum, 0, indices, Ninds, destination, dest_stride, 1); } int qfits_query_column_seq_to_array_no_endian_swap( const qfits_table * th, int colnum, int start_ind, int nb_rows, unsigned char* destination, int dest_stride) { return qfits_query_column_seq_to_array_endian(th, colnum, start_ind, NULL, nb_rows, destination, dest_stride, 0); } /*----------------------------------------------------------------------------*/ /** @brief Extract binary data from a column in a FITS table @param th Allocated qfits_table @param colnum Number of the column to extract (from 0 to colnum-1) @param selection bollean array to identify selected rows @param null_value Value to return when a NULL value comes @return Pointer to void * Extract a column from a FITS table and return the data as a generic void* array. The returned array type and size are determined by the column object in the qfits_table. Returned array size in bytes is: nb_selected * col->atom_nb * col->atom_size NULL values are recognized and replaced by the specified value. The returned object must be deallocated with qfits_free(). */ /*----------------------------------------------------------------------------*/ void * qfits_query_column_data( const qfits_table * th, int colnum, const int * selection, const void * null_value) { void * out_array; qfits_col * col; int nb_rows; unsigned char * in_array; char * field; unsigned char ucnull; short snull; int inull; double dnull; float fnull; int i; /* Initialize */ if (null_value == NULL) { inull = (int)0; snull = (short)0; ucnull = (unsigned char)0; fnull = (float)0.0; dnull = (double)0.0; } else { inull = *(int*)null_value; snull = *(short*)null_value; ucnull = *(unsigned char*)null_value; fnull = *(float*)null_value; dnull = *(double*)null_value; } /* Get the number of selected rows */ nb_rows = 0; if (selection == NULL) { nb_rows = th->nr; } else { for (i=0; inr; i++) if (selection[i] == 1) nb_rows++; } /* Pointer to requested column */ col = th->col+colnum; /* Test if column is readable */ if (col->readable == 0) return NULL; /* Handle each type separately */ switch(col->atom_type) { case TFITS_ASCII_TYPE_A: out_array = (char*)qfits_query_column(th, colnum, selection); break; case TFITS_ASCII_TYPE_I: in_array = (unsigned char*)qfits_query_column(th, colnum, selection); out_array = qfits_malloc(nb_rows*col->atom_size); field = qfits_malloc((col->atom_nb+1)*sizeof(char)); for (i=0; iatom_nb], col->atom_nb); field[col->atom_nb]='\0'; /* Write the data in out_array */ /* Test if a NULL val is encoutered */ if (!strcmp(col->nullval, qfits_strstrip(field))) { ((int*)out_array)[i] = inull; } else { ((int*)out_array)[i] = (int)atoi(field); } } qfits_free(field); qfits_free(in_array); break; case TFITS_ASCII_TYPE_E: case TFITS_ASCII_TYPE_F: in_array = (unsigned char*)qfits_query_column(th, colnum, selection); out_array = qfits_malloc(nb_rows*col->atom_size); field = qfits_malloc((col->atom_nb+1)*sizeof(char)); for (i=0; iatom_nb], col->atom_nb); field[col->atom_nb]='\0'; /* Write the data in out_array */ /* Test if a NULL val is encoutered */ if (!strcmp(col->nullval, qfits_strstrip(field))) { ((float*)out_array)[i] = fnull; } else { /* Add the decimal handling */ ((float*)out_array)[i]=(float)qfits_str2dec(field, col->atom_dec_nb); } } qfits_free(field); qfits_free(in_array); break; case TFITS_ASCII_TYPE_D: in_array = (unsigned char*)qfits_query_column(th, colnum, selection); out_array = qfits_malloc(nb_rows*col->atom_size); field = qfits_malloc((col->atom_nb+1)*sizeof(char)); for (i=0; iatom_nb], col->atom_nb); field[col->atom_nb]='\0'; /* Write the data in out_array */ /* Test if a NULL val is encoutered */ if (!strcmp(col->nullval, field)) { ((double*)out_array)[i] = dnull; } else { /* Add the decimal handling */ ((double*)out_array)[i]=qfits_str2dec(field, col->atom_dec_nb); } } qfits_free(field); qfits_free(in_array); break; case TFITS_BIN_TYPE_A: case TFITS_BIN_TYPE_L: out_array = (char*)qfits_query_column(th, colnum, selection); break; case TFITS_BIN_TYPE_D: case TFITS_BIN_TYPE_M: out_array = (double*)qfits_query_column(th, colnum, selection); for (i=0; iatom_nb; i++) { if (qfits_isnan(((double*)out_array)[i]) || qfits_isinf(((double*)out_array)[i])) { ((double*)out_array)[i] = dnull; } } break; case TFITS_BIN_TYPE_E: case TFITS_BIN_TYPE_C: out_array = (float*)qfits_query_column(th, colnum, selection); for (i=0; iatom_nb; i++) { if (qfits_isnan(((float*)out_array)[i]) || qfits_isinf(((float*)out_array)[i])) { ((float*)out_array)[i] = fnull; } } break; case TFITS_BIN_TYPE_X: out_array = (unsigned char*)qfits_query_column(th, colnum, selection); break; case TFITS_BIN_TYPE_B: out_array = (unsigned char*)qfits_query_column(th, colnum, selection); for (i=0; iatom_nb; i++) { if (((col->nullval)[0] != '\0') && (atoi(col->nullval) == (int)((unsigned char*)out_array)[i])) { ((unsigned char*)out_array)[i] = ucnull; } } break; case TFITS_BIN_TYPE_I: out_array = (short*)qfits_query_column(th, colnum, selection); for (i=0; iatom_nb; i++) { if (((col->nullval)[0] != '\0') && (atoi(col->nullval)==(int)((short*)out_array)[i])) { ((short*)out_array)[i] = snull; } } break; case TFITS_BIN_TYPE_J: out_array = (int*)qfits_query_column(th, colnum, selection); for (i=0; iatom_nb; i++) { if (((col->nullval)[0] != '\0') && (atoi(col->nullval)==((int*)out_array)[i])) { ((int*)out_array)[i] = inull; } } break; case TFITS_BIN_TYPE_K: out_array = (int64_t*)qfits_query_column(th, colnum, selection); for (i=0; iatom_nb; i++) { if (((col->nullval)[0] != '\0') && (atoll(col->nullval)==((int64_t*)out_array)[i])) { ((int64_t*)out_array)[i] = inull; } } break; case TFITS_BIN_TYPE_P: out_array = (int*)qfits_query_column(th, colnum, selection); break; default: qfits_error("unrecognized data type"); return NULL; } return out_array; } /*----------------------------------------------------------------------------*/ /** @brief Extract binary data from a column in a FITS table @param th Allocated qfits_table @param colnum Number of the column to extract (from 0 to colnum-1) @param start_ind Index of the first row (0 for the first) @param nb_rows Number of rows to extract @param null_value Value to return when a NULL value comes @return Pointer to void * Does the same as qfits_query_column_data() but on a consequtive sequence of rows. Spares the overhead of the selection object allocation The returned object must be deallocated with qfits_free(). */ /*----------------------------------------------------------------------------*/ void * qfits_query_column_seq_data( const qfits_table * th, int colnum, int start_ind, int nb_rows, const void * null_value) { void * out_array; qfits_col * col; unsigned char * in_array; char * field; unsigned char ucnull; short snull; int inull; double dnull; float fnull; int i; /* Initialize */ if (null_value == NULL) { inull = (int)0; snull = (short)0; ucnull = (unsigned char)0; fnull = (float)0.0; dnull = (double)0.0; } else { inull = *(int*)null_value; snull = *(short*)null_value; ucnull = *(unsigned char*)null_value; fnull = *(float*)null_value; dnull = *(double*)null_value; } /* Pointer to requested column */ col = th->col+colnum; /* Test if column is readable */ if (col->readable == 0) return NULL; /* Handle each type separately */ switch(col->atom_type) { case TFITS_ASCII_TYPE_A: out_array = (char*)qfits_query_column_seq(th, colnum, start_ind, nb_rows); break; case TFITS_ASCII_TYPE_I: in_array = (unsigned char*)qfits_query_column_seq(th, colnum, start_ind, nb_rows); out_array = qfits_malloc(nb_rows*col->atom_size); field = qfits_malloc((col->atom_nb+1)*sizeof(char)); for (i=0; iatom_nb], col->atom_nb); field[col->atom_nb]='\0'; /* Write the data in out_array */ /* Test if a NULL val is encoutered */ if (!strcmp(col->nullval, qfits_strstrip(field))) { ((int*)out_array)[i] = inull; } else { ((int*)out_array)[i] = (int)atoi(field); } } qfits_free(field); qfits_free(in_array); break; case TFITS_ASCII_TYPE_E: case TFITS_ASCII_TYPE_F: in_array = (unsigned char*)qfits_query_column_seq(th, colnum, start_ind, nb_rows); out_array = qfits_malloc(nb_rows*col->atom_size); field = qfits_malloc((col->atom_nb+1)*sizeof(char)); for (i=0; iatom_nb], col->atom_nb); field[col->atom_nb]='\0'; /* Write the data in out_array */ /* Test if a NULL val is encoutered */ if (!strcmp(col->nullval, qfits_strstrip(field))) { ((float*)out_array)[i] = fnull; } else { /* Add the decimal handling */ ((float*)out_array)[i]=(float)qfits_str2dec(field, col->atom_dec_nb); } } qfits_free(field); qfits_free(in_array); break; case TFITS_ASCII_TYPE_D: in_array = (unsigned char*)qfits_query_column_seq(th, colnum, start_ind, nb_rows); out_array = qfits_malloc(nb_rows*col->atom_size); field = qfits_malloc((col->atom_nb+1)*sizeof(char)); for (i=0; iatom_nb], col->atom_nb); field[col->atom_nb]='\0'; /* Write the data in out_array */ /* Test if a NULL val is encoutered */ if (!strcmp(col->nullval, qfits_strstrip(field))) { ((double*)out_array)[i] = dnull; } else { /* Add the decimal handling */ ((double*)out_array)[i]=qfits_str2dec(field, col->atom_dec_nb); } } qfits_free(field); qfits_free(in_array); break; case TFITS_BIN_TYPE_A: case TFITS_BIN_TYPE_L: out_array = (char*)qfits_query_column_seq(th, colnum, start_ind, nb_rows); break; case TFITS_BIN_TYPE_D: case TFITS_BIN_TYPE_M: out_array = (double*)qfits_query_column_seq(th, colnum, start_ind, nb_rows); for (i=0; iatom_nb; i++) { if (qfits_isnan(((double*)out_array)[i]) || qfits_isinf(((double*)out_array)[i])) { ((double*)out_array)[i] = dnull; } } break; case TFITS_BIN_TYPE_E: case TFITS_BIN_TYPE_C: out_array = (float*)qfits_query_column_seq(th, colnum, start_ind, nb_rows); for (i=0; iatom_nb; i++) { if (qfits_isnan(((float*)out_array)[i]) || qfits_isinf(((float*)out_array)[i])) { ((float*)out_array)[i] = fnull; } } break; case TFITS_BIN_TYPE_X: out_array = (unsigned char*)qfits_query_column_seq(th, colnum, start_ind, nb_rows); break; case TFITS_BIN_TYPE_B: out_array = (unsigned char*)qfits_query_column_seq(th, colnum, start_ind, nb_rows); for (i=0; iatom_nb; i++) { if (((col->nullval)[0] != '\0') && (atoi(col->nullval)== (int)((unsigned char*)out_array)[i])) { ((unsigned char*)out_array)[i] = ucnull; } } break; case TFITS_BIN_TYPE_I: out_array = (short*)qfits_query_column_seq(th, colnum, start_ind, nb_rows); for (i=0; iatom_nb; i++) { if (((col->nullval)[0] != '\0') && (atoi(col->nullval)==(int)((short*)out_array)[i])) { ((short*)out_array)[i] = snull; } } break; case TFITS_BIN_TYPE_J: out_array = (int*)qfits_query_column_seq(th, colnum, start_ind, nb_rows); for (i=0; iatom_nb; i++) { if (((col->nullval)[0] != '\0') && (atoi(col->nullval)==((int*)out_array)[i])) { ((int*)out_array)[i] = inull; } } break; case TFITS_BIN_TYPE_K: out_array = (int64_t*)qfits_query_column_seq(th, colnum, start_ind, nb_rows); for (i=0; iatom_nb; i++) { if (((col->nullval)[0] != '\0') && (atoll(col->nullval)==((int64_t*)out_array)[i])) { ((int64_t*)out_array)[i] = inull; } } break; case TFITS_BIN_TYPE_P: out_array = (int*)qfits_query_column_seq(th, colnum, start_ind, nb_rows); break; default: qfits_error("unrecognized data type"); return NULL; } return out_array; } /*----------------------------------------------------------------------------*/ /** @brief Detect NULL values in a column @param th Allocated qfits_table @param colnum Number of the column to check (from 0 to colnum-1) @param selection Array to identify selected rows @param nb_vals Gives the size of the output array @param nb_nulls Gives the number of detected null values @return array with 1 for NULLs and 0 for non-NULLs The returned object must be deallocated with qfits_free(). */ /*----------------------------------------------------------------------------*/ int * qfits_query_column_nulls( const qfits_table * th, int colnum, const int * selection, int * nb_vals, int * nb_nulls) { int * out_array; qfits_col * col; unsigned char * in_array; void * tmp_array; char * field; int nb_rows; int i; /* Initialize */ *nb_nulls = 0; *nb_vals = 0; /* Get the number of selected rows */ nb_rows = 0; if (selection == NULL) { nb_rows = th->nr; } else { for (i=0; inr; i++) if (selection[i] == 1) nb_rows++; } /* Pointer to requested column */ col = th->col+colnum; /* Test if column is readable */ if (col->readable == 0) return NULL; /* Handle each type separately */ switch(col->atom_type) { case TFITS_ASCII_TYPE_A: case TFITS_ASCII_TYPE_D: case TFITS_ASCII_TYPE_E: case TFITS_ASCII_TYPE_F: case TFITS_ASCII_TYPE_I: in_array = (unsigned char*)qfits_query_column(th, colnum, selection); out_array = qfits_calloc(nb_rows, sizeof(int)); *nb_vals = nb_rows; field = qfits_malloc((col->atom_nb+1)*sizeof(char)); for (i=0; iatom_nb], col->atom_nb); field[col->atom_nb]='\0'; /* Test if a NULL val is encoutered */ if (!strcmp(col->nullval, qfits_strstrip(field))) { out_array[i] = 1; (*nb_nulls)++; } } qfits_free(field); if (in_array != NULL) qfits_free(in_array); break; case TFITS_BIN_TYPE_A: /* No NULL values */ out_array = qfits_calloc(nb_rows * col->atom_nb, sizeof(int)); *nb_vals = nb_rows * col->atom_nb; break; case TFITS_BIN_TYPE_L: case TFITS_BIN_TYPE_X: case TFITS_BIN_TYPE_P: /* No NULL values */ out_array = qfits_calloc(nb_rows * col->atom_nb, sizeof(int)); *nb_vals = nb_rows * col->atom_nb; break; case TFITS_BIN_TYPE_D: case TFITS_BIN_TYPE_M: tmp_array = (double*)qfits_query_column(th, colnum, selection); out_array = qfits_calloc(nb_rows * col->atom_nb, sizeof(int)); *nb_vals = nb_rows * col->atom_nb; for (i=0; iatom_nb; i++) { if (qfits_isnan(((double*)tmp_array)[i]) || qfits_isinf(((double*)tmp_array)[i])) { out_array[i] = 1; (*nb_nulls)++; } } if (tmp_array != NULL) qfits_free(tmp_array); break; case TFITS_BIN_TYPE_E: case TFITS_BIN_TYPE_C: tmp_array = (float*)qfits_query_column(th, colnum, selection); out_array = qfits_calloc(nb_rows * col->atom_nb, sizeof(int)); *nb_vals = nb_rows * col->atom_nb; for (i=0; iatom_nb; i++) { if (qfits_isnan(((float*)tmp_array)[i]) || qfits_isinf(((float*)tmp_array)[i])) { out_array[i] = 1; (*nb_nulls)++; } } if (tmp_array != NULL) qfits_free(tmp_array); break; case TFITS_BIN_TYPE_B: tmp_array = (unsigned char*)qfits_query_column(th, colnum, selection); out_array = qfits_calloc(nb_rows * col->atom_nb, sizeof(int)); *nb_vals = nb_rows * col->atom_nb; for (i=0; iatom_nb; i++) { if (((col->nullval)[0] != '\0') && (atoi(col->nullval)==(int)((unsigned char*)tmp_array)[i])) { out_array[i] = 1; (*nb_nulls)++; } } if (tmp_array != NULL) qfits_free(tmp_array); break; case TFITS_BIN_TYPE_I: tmp_array = (short*)qfits_query_column(th, colnum, selection); out_array = qfits_calloc(nb_rows * col->atom_nb, sizeof(int)); *nb_vals = nb_rows * col->atom_nb; for (i=0; iatom_nb; i++) { if (((col->nullval)[0] != '\0') && (atoi(col->nullval)==(int)((short*)tmp_array)[i])) { out_array[i] = 1; (*nb_nulls)++; } } if (tmp_array != NULL) qfits_free(tmp_array); break; case TFITS_BIN_TYPE_K: tmp_array = (int64_t*)qfits_query_column(th, colnum, selection); out_array = calloc(nb_rows * col->atom_nb, sizeof(int64_t)); *nb_vals = nb_rows * col->atom_nb; for (i=0; iatom_nb; i++) { if (((col->nullval)[0] != '\0') && (atoll(col->nullval)==((int64_t*)tmp_array)[i])) { out_array[i] = 1; (*nb_nulls)++; } } if (tmp_array != NULL) free(tmp_array); break; case TFITS_BIN_TYPE_J: tmp_array = (int*)qfits_query_column(th, colnum, selection); out_array = qfits_calloc(nb_rows * col->atom_nb, sizeof(int)); *nb_vals = nb_rows * col->atom_nb; for (i=0; iatom_nb; i++) { if (((col->nullval)[0] != '\0') && (atoi(col->nullval)==((int*)tmp_array)[i])) { out_array[i] = 1; (*nb_nulls)++; } } if (tmp_array != NULL) qfits_free(tmp_array); break; default: qfits_error("unrecognized data type"); return NULL; } return out_array; } /*----------------------------------------------------------------------------*/ /** @brief Appends a std extension header + data to a FITS table file. @param outfile Pointer to (opened) file ready for writing. @param t Pointer to qfits_table @param data Table data to write @return int 0 if Ok, -1 otherwise Dumps a FITS table to a file. The whole table described by qfits_table, and the data arrays contained in 'data' are dumped to the file. An extension header is produced with all keywords needed to describe the table, then the data is dumped to the file. The output is then padded to reach a multiple of 2880 bytes in size. Notice that no main header is produced, only the extension part. */ /*----------------------------------------------------------------------------*/ int qfits_table_append_xtension( FILE * outfile, const qfits_table * t, const void ** data) { /* Append the extension */ if (t->tab_t == QFITS_BINTABLE) { if (qfits_table_append_bin_xtension(outfile, t, data) == -1) { qfits_error("in writing fits table"); return -1; } } else if (t->tab_t == QFITS_ASCIITABLE) { if (qfits_table_append_ascii_xtension(outfile, t, data) == -1) { qfits_error("in writing fits table"); return -1; } } else { qfits_error("Unrecognized table type"); return -1; } return 0; } /*----------------------------------------------------------------------------*/ /** @brief Appends a specified extension header + data to a FITS table file. @param outfile Pointer to (opened) file ready for writing. @param t Pointer to qfits_table @param data Table data to write @param hdr Specified extension header @return int 0 if Ok, -1 otherwise Dumps a FITS table to a file. The whole table described by qfits_table, and the data arrays contained in 'data' are dumped to the file following the specified fits header. The output is then padded to reach a multiple of 2880 bytes in size. Notice that no main header is produced, only the extension part. */ /*----------------------------------------------------------------------------*/ int qfits_table_append_xtension_hdr( FILE * outfile, const qfits_table * t, const void ** data, const qfits_header * hdr) { /* Write the fits header in the file */ if (qfits_header_dump(hdr, outfile) == -1) { qfits_error("cannot dump header in file"); return -1; } /* Append the data to the file */ return qfits_table_append_data(outfile, t, data); } /*----------------------------------------------------------------------------*/ /** @brief given a col and a row, find out the string to write for display @param table table structure @param col_id col id (0 -> nbcol-1) @param row_id row id (0 -> nrow-1) @param use_zero_scale Flag to use or not zero and scale @return the string This function is highly inefficient, it should not be used in loops to display a complete table. It is more to get one field from time to time, or for debugging puposes. The returned object must be deallocated with qfits_free(). */ /*----------------------------------------------------------------------------*/ char * qfits_table_field_to_string( const qfits_table * table, int col_id, int row_id, int use_zero_scale) { char * str; switch (table->tab_t) { case QFITS_BINTABLE: str = qfits_bintable_field_to_string(table, col_id, row_id, use_zero_scale); break; case QFITS_ASCIITABLE: str = qfits_asciitable_field_to_string(table, col_id, row_id, use_zero_scale); break; default: qfits_error("Table type not recognized"); return NULL; break; } return str; } /**@}*/ /*----------------------------------------------------------------------------*/ /** @brief Compute the table width in bytes from the columns infos @param th Allocated qfits_table @return the width (-1 in error case) */ /*----------------------------------------------------------------------------*/ int qfits_compute_table_width(const qfits_table * th) { int width; qfits_col * curr_col; int i; /* Initialize */ width = 0; /* Loop on all columns and get column descriptions */ curr_col = th->col; for (i=0; inc; i++) { if (th->tab_t == QFITS_ASCIITABLE) { width += curr_col->atom_nb; } else if (th->tab_t == QFITS_BINTABLE) { width += curr_col->atom_nb * curr_col->atom_size; } curr_col++; } return width; } /*----------------------------------------------------------------------------*/ /** @brief given a col and a row, find out the string to write for display @param table table structure @param col_id col id (0 -> nbcol-1) @param row_id row id (0 -> nrow-1) @param use_zero_scale Flag to use or not zero and scale @return the string to write The returned object must be deallocated with qfits_free(). ASCII tables specific */ /*----------------------------------------------------------------------------*/ static char * qfits_asciitable_field_to_string( const qfits_table * table, int col_id, int row_id, int use_zero_scale) { qfits_col * col; char * ccol; int * icol; float * fcol; double * dcol; char ctmp[512]; char * stmp; int field_size; void * field; int * selection; /* Test inputs */ if (table->tab_t != QFITS_ASCIITABLE) return NULL; /* Initialize */ ctmp[0] = '\0'; /* Set selection to select the requested row */ selection = qfits_calloc(table->nr, sizeof(int)); selection[row_id] = 1; /* Load the column data */ if ((field = qfits_query_column_data(table, col_id, selection, NULL)) == NULL) return NULL; qfits_free(selection); /* Set reference to the column */ col = table->col + col_id; /* Compute field size and allocate stmp */ if (col->atom_nb > ELEMENT_MAX_DISPLAY_SIZE) field_size = col->atom_nb + 1; else field_size = ELEMENT_MAX_DISPLAY_SIZE; stmp = qfits_malloc(field_size * sizeof(char)); stmp[0] = '\0'; /* Get the string to write according to the type */ switch(col->atom_type) { case TFITS_ASCII_TYPE_A: ccol = (char*)field; strncpy(ctmp, ccol, col->atom_nb); ctmp[col->atom_nb] = '\0'; strcpy(stmp, ctmp); break; case TFITS_ASCII_TYPE_I: icol = (int*)field; /* Two cases: use col->zero and col->scale or not */ if (col->zero_present && col->scale_present && use_zero_scale) { sprintf(stmp, "%f", (float)(col->zero + (float)icol[0] * col->scale)); } else { sprintf(stmp, "%d", icol[0]); } break; case TFITS_ASCII_TYPE_E: case TFITS_ASCII_TYPE_F: fcol = (float*)field; /* Two cases: use col->zero and col->scale or not */ if (col->zero_present && col->scale_present && use_zero_scale) { sprintf(stmp, "%f", (float)(col->zero + fcol[0] * col->scale)); } else { sprintf(stmp, "%f", fcol[0]); } break; case TFITS_ASCII_TYPE_D: dcol = (double*)field; /* Two cases: use col->zero and col->scale or not */ if (col->zero_present && col->scale_present && use_zero_scale) { sprintf(stmp, "%f", (float)(col->zero + (float)dcol[0] * col->scale)); } else { sprintf(stmp, "%g", dcol[0]); } break; default: qfits_warning("Type not recognized"); break; } /* Free and return */ qfits_free(field); return stmp; } /*----------------------------------------------------------------------------*/ /** @brief Given a col and a row, find out the string to write for display @param table table structure @param col_id col id (0 -> nbcol-1) @param row_id row id (0 -> nrow-1) @param use_zero_scale Flag to use or not zero and scale @return the allocated string to write The returned object must be deallocated with qfits_free(). BIN tables specific */ /*----------------------------------------------------------------------------*/ static char * qfits_bintable_field_to_string( const qfits_table * table, int col_id, int row_id, int use_zero_scale) { qfits_col * col; unsigned char * uccol; char * ccol; int * icol; int64_t * kcol; short * scol; float * fcol; double * dcol; char ctmp[512]; char * stmp; int field_size; void * field; int * selection; int i; /* Test inputs */ if (table->tab_t != QFITS_BINTABLE) return NULL; /* Initialize */ ctmp[0] = '\0'; /* Set selection to select the requested row */ selection = qfits_calloc(table->nr, sizeof(int)); selection[row_id] = 1; /* Load the data column */ if ((field = qfits_query_column_data(table, col_id, selection, NULL)) == NULL) { qfits_free(selection); return NULL; } qfits_free(selection); /* Set reference to the column */ col = table->col + col_id; /* Compute field size and allocate stmp */ field_size = col->atom_nb * ELEMENT_MAX_DISPLAY_SIZE; stmp = qfits_malloc(field_size * sizeof(char)); stmp[0] = '\0'; /* Get the string to write according to the type */ switch(col->atom_type) { case TFITS_BIN_TYPE_A: ccol = (char*)field; strncpy(ctmp, ccol, col->atom_size * col->atom_nb); ctmp[col->atom_size*col->atom_nb] = '\0'; strcpy(stmp, ctmp); break; case TFITS_BIN_TYPE_B: uccol = (unsigned char*)field; /* Two cases: use col->zero and col->scale or not */ if (col->zero_present && col->scale_present && use_zero_scale) { /* For each atom of the column */ for (i=0; iatom_nb-1; i++) { sprintf(ctmp, "%f, ", (float)(col->zero + (float)uccol[i] * col->scale)); strcat(stmp, ctmp); } /* Handle the last atom differently: no ',' */ sprintf(ctmp, "%f", (float)(col->zero + (float)uccol[col->atom_nb-1]*col->scale)); strcat(stmp, ctmp); } else { /* For each atom of the column */ for (i=0; iatom_nb-1; i++) { sprintf(ctmp, "%d, ", (int)uccol[i]); strcat(stmp, ctmp); } /* Handle the last atom differently: no ',' */ sprintf(ctmp,"%d",(int)uccol[col->atom_nb-1]); strcat(stmp, ctmp); } break; case TFITS_BIN_TYPE_D: case TFITS_BIN_TYPE_M: dcol = (double*)field; /* Two cases: use col->zero and col->scale or not */ if (col->zero_present && col->scale_present && use_zero_scale) { /* For each atom of the column */ for (i=0; iatom_nb-1; i++) { sprintf(ctmp, "%g, ", (double)((double)col->zero + dcol[i] * (double)col->scale)); strcat(stmp, ctmp); } /* Handle the last atom differently: no ',' */ sprintf(ctmp, "%g", (double)((double)col->zero + dcol[col->atom_nb-1] * (double)col->scale)); strcat(stmp, ctmp); } else { /* For each atom of the column */ for (i=0; iatom_nb-1; i++) { sprintf(ctmp, "%g, ", dcol[i]); strcat(stmp, ctmp); } /* Handle the last atom differently: no ',' */ sprintf(ctmp, "%g", dcol[col->atom_nb-1]); strcat(stmp, ctmp); } break; case TFITS_BIN_TYPE_E: case TFITS_BIN_TYPE_C: fcol = (float*)field; /* Two cases: use col->zero and col->scale or not */ if (col->zero_present && col->scale_present && use_zero_scale) { /* For each atom of the column */ for (i=0; iatom_nb-1; i++) { sprintf(ctmp, "%f, ", (float)(col->zero + (float)fcol[i] * col->scale)); strcat(stmp, ctmp); } /* Handle the last atom differently: no ',' */ sprintf(ctmp, "%f", (float)(col->zero + (float)fcol[col->atom_nb-1] * col->scale)); strcat(stmp, ctmp); } else { /* For each atom of the column */ for (i=0; iatom_nb-1; i++) { sprintf(ctmp, "%f, ", fcol[i]); strcat(stmp, ctmp); } /* Handle the last atom differently: no ',' */ sprintf(ctmp, "%f", fcol[col->atom_nb-1]); strcat(stmp, ctmp); } break; case TFITS_BIN_TYPE_I: scol = (short*)field; /* Two cases: use col->zero and col->scale or not */ if (col->zero_present && col->scale_present && use_zero_scale) { /* For each atom of the column */ for (i=0; iatom_nb-1; i++) { sprintf(ctmp, "%f, ", (float)(col->zero + (float)scol[i] * col->scale)); strcat(stmp, ctmp); } /* Handle the last atom differently: no ',' */ sprintf(ctmp, "%f", (float)(col->zero + (float)scol[col->atom_nb-1] * col->scale)); strcat(stmp, ctmp); } else { /* For each atom of the column */ for (i=0; iatom_nb-1; i++) { sprintf(ctmp, "%d, ", (int)scol[i]); strcat(stmp, ctmp); } /* Handle the last atom differently: no ',' */ sprintf(ctmp, "%d",(int)scol[col->atom_nb-1]); strcat(stmp, ctmp); } break; case TFITS_BIN_TYPE_J: icol = (int*)field; /* Two cases: use col->zero and col->scale or not */ if (col->zero_present && col->scale_present && use_zero_scale) { /* For each atom of the column */ for (i=0; iatom_nb-1; i++) { sprintf(ctmp, "%f, ", (float)(col->zero + (float)icol[i] * col->scale)); strcat(stmp, ctmp); } /* Handle the last atom differently: no ',' */ sprintf(ctmp, "%f", (float)(col->zero + (float)icol[col->atom_nb-1] * col->scale)); strcat(stmp, ctmp); } else { /* For each atom of the column */ for (i=0; iatom_nb-1; i++) { sprintf(ctmp, "%d, ", (int)icol[i]); strcat(stmp, ctmp); } /* Handle the last atom differently: no ',' */ sprintf(ctmp, "%d",(int)icol[col->atom_nb-1]); strcat(stmp, ctmp); } break; case TFITS_BIN_TYPE_K: kcol = (int64_t*)field; /* Two cases: use col->zero and col->scale or not */ if (col->zero_present && col->scale_present && use_zero_scale) { /* For each atom of the column */ for (i=0; iatom_nb-1; i++) { sprintf(ctmp, "%f, ", (float)(col->zero + (float)kcol[i] * col->scale)); strcat(stmp, ctmp); } /* Handle the last atom differently: no ',' */ sprintf(ctmp, "%f", (float)(col->zero + (float)kcol[col->atom_nb-1] * col->scale)); strcat(stmp, ctmp); } else { /* For each atom of the column */ for (i=0; iatom_nb-1; i++) { sprintf(ctmp, "%lld, ", (long long int)kcol[i]); strcat(stmp, ctmp); } /* Handle the last atom differently: no ',' */ sprintf(ctmp, "%lld", (long long int)kcol[col->atom_nb-1]); strcat(stmp, ctmp); } break; case TFITS_BIN_TYPE_L: ccol = (char*)field; /* For each atom of the column */ for (i=0; iatom_nb-1; i++) { sprintf(ctmp, "%c, ", ccol[i]); strcat(stmp, ctmp); } /* Handle the last atom differently: no ',' */ sprintf(ctmp, "%c", ccol[col->atom_nb-1]); strcat(stmp, ctmp); break; case TFITS_BIN_TYPE_X: uccol = (unsigned char*)field; /* For each atom of the column */ for (i=0; iatom_nb-1; i++) { sprintf(ctmp, "%d, ", uccol[i]); strcat(stmp, ctmp); } /* Handle the last atom differently: no ',' */ sprintf(ctmp, "%d", uccol[col->atom_nb-1]); strcat(stmp, ctmp); break; case TFITS_BIN_TYPE_P: icol = (int*)field; /* For each atom of the column */ for (i=0; iatom_nb-1; i++) { sprintf(ctmp, "%d, ", (int)icol[i]); strcat(stmp, ctmp); } /* Handle the last atom differently: no ',' */ sprintf(ctmp, "%d",(int)icol[col->atom_nb-1]); strcat(stmp, ctmp); break; default: qfits_warning("Type not recognized"); break; } qfits_free(field); return stmp; } /*----------------------------------------------------------------------------*/ /** @brief Remove blanks at the beginning and the end of a string. @param s String to parse. @return ptr to statically allocated string. This function returns a pointer to a statically allocated string, which is identical to the input string, except that all blank characters at the end and the beg. of the string have been removed. Do not free or modify the returned string! Since the returned string is statically allocated, it will be modified at each function call (not re-entrant). */ /*----------------------------------------------------------------------------*/ static char * qfits_strstrip(const char * s) { static char l[1024+1]; char * last; if (s==NULL) return NULL; while (isspace((int)*s) && *s) s++; memset(l, 0, 1024+1); strcpy(l, s); last = l + strlen(l); while (last > l) { if (!isspace((int)*(last-1))) break; last --; } *last = '\0'; return (char*)l; } /*----------------------------------------------------------------------------*/ /** @brief Make a double out of a string and a number of decimals @param to_format the string to convert @param nb_dec the number of decimals @return the double A field with 123 of type F3.1 actually contains 12.3 This is handled by this function. */ /*----------------------------------------------------------------------------*/ static double qfits_str2dec( const char * to_format, int nb_dec) { double val; int i; /* Test entries */ if (to_format == NULL) return 0.00; val = (double)atof(to_format); /* First handle case where there are no decimals or the dot is there */ if ((strstr(to_format, ".") == NULL) && (nb_dec > 0)) { for (i=0; iatom_type) { case TFITS_ASCII_TYPE_A: nb=sprintf(sval, "A%d.%d", col->atom_nb, col->atom_dec_nb); break; case TFITS_ASCII_TYPE_D: nb=sprintf(sval, "D%d.%d", col->atom_nb, col->atom_dec_nb); break; case TFITS_ASCII_TYPE_E: nb=sprintf(sval, "E%d.%d", col->atom_nb, col->atom_dec_nb); break; case TFITS_ASCII_TYPE_I: nb=sprintf(sval, "I%d.%d", col->atom_nb, col->atom_dec_nb); break; case TFITS_ASCII_TYPE_F: nb=sprintf(sval, "F%d.%d", col->atom_nb, col->atom_dec_nb); break; case TFITS_BIN_TYPE_D: nb=sprintf(sval, "%dD", col->atom_nb); break; case TFITS_BIN_TYPE_E: nb=sprintf(sval, "%dE", col->atom_nb); break; case TFITS_BIN_TYPE_I: nb=sprintf(sval, "%dI", col->atom_nb); break; case TFITS_BIN_TYPE_A: nb=sprintf(sval, "%dA", col->atom_nb); break; case TFITS_BIN_TYPE_B: nb=sprintf(sval, "%dB", col->atom_nb); break; case TFITS_BIN_TYPE_C: nb=sprintf(sval, "%dC", (int)(col->atom_nb/2)); break; case TFITS_BIN_TYPE_J: nb=sprintf(sval, "%dJ", col->atom_nb); break; case TFITS_BIN_TYPE_K: nb=sprintf(sval, "%dK", col->atom_nb); break; case TFITS_BIN_TYPE_L: nb=sprintf(sval, "%dL", col->atom_nb); break; case TFITS_BIN_TYPE_M: nb=sprintf(sval, "%dM", (int)(col->atom_nb/2)); break; case TFITS_BIN_TYPE_P: nb=sprintf(sval, "%dP", (int)(col->atom_nb/2)); break; case TFITS_BIN_TYPE_X: nb=sprintf(sval, "%dX", 8*col->atom_nb); break; default: return NULL; } sval[nb] = '\0'; return sval; } /*----------------------------------------------------------------------------*/ /** @brief Appends a std extension header + data to a FITS BIN table file. @param outfile Pointer to (opened) file ready for writing. @param t Pointer to qfits_table @param data Table data to write @return int 0 if Ok, -1 otherwise Dumps a FITS table to a file. The whole table described by qfits_table, and the data arrays contained in 'data' are dumped to the file. An extension header is produced with all keywords needed to describe the table, then the data is dumped to the file. The output is then padded to reach a multiple of 2880 bytes in size. Notice that no main header is produced, only the extension part. */ /*----------------------------------------------------------------------------*/ static int qfits_table_append_bin_xtension( FILE * outfile, const qfits_table * t, const void ** data) { qfits_header * fh; if ((fh=qfits_table_ext_header_default(t)) == NULL) { qfits_error("cannot create new fits header"); return -1; } /* Write the fits header in the file */ if (qfits_header_dump(fh, outfile) == -1) { qfits_error("cannot dump header in file"); qfits_header_destroy(fh); fclose(outfile); return -1; } qfits_header_destroy(fh); /* Append the data to the file */ return qfits_table_append_data(outfile, t, data); } /*----------------------------------------------------------------------------*/ /** @brief Appends an extension header + data to a FITS ASCII table file. @param outfile Pointer to (opened) file ready for writing. @param t Pointer to qfits_table @param data Table data to write @return int 0 if Ok, -1 otherwise Dumps a FITS table to a file. The whole table described by qfits_table, and the data arrays contained in 'data' are dumped to the file. An extension header is produced with all keywords needed to describe the table, then the data is dumped to the file. The output is then padded to reach a multiple of 2880 bytes in size. Notice that no main header is produced, only the extension part. */ /*----------------------------------------------------------------------------*/ static int qfits_table_append_ascii_xtension( FILE * outfile, const qfits_table * t, const void ** data) { qfits_header * fh; if ((fh=qfits_table_ext_header_default(t)) == NULL) { qfits_error("cannot create new fits header"); return -1; } /* Write the fits header in the file */ if (qfits_header_dump(fh, outfile) == -1) { qfits_error("cannot dump header in file"); qfits_header_destroy(fh); return -1; } qfits_header_destroy(fh); /* Append the data to the file */ return qfits_table_append_data(outfile, t, data); } /*----------------------------------------------------------------------------*/ /** @brief Appends data to a FITS table file. @param outfile Pointer to (opened) file ready for writing. @param t Pointer to qfits_table @param data Table data to write @return int 0 if Ok, -1 otherwise Dumps the data part of a FITS table to a file. The primary header, as well as the extension header are supposed to be already there (and properly padded). The output is then padded to reach a multiple of 2880 bytes in size. */ /*----------------------------------------------------------------------------*/ static int qfits_table_append_data( FILE * outfile, const qfits_table * t, const void ** data) { qfits_col * curr_col; char field[1024]; char * line; unsigned char ** array; unsigned char * r; unsigned char * inbuf; int writt_char; int nb_blanks; int field_size; int i, j; /* Write DATA */ array = qfits_malloc(t->nc*sizeof(unsigned char *)); curr_col = t->col; for (i=0; inc; i++) { /* Compute the field size */ field_size = qfits_table_get_field_size(t->tab_t, curr_col); /* Copy data from data to array (unsigned char) */ array[i] = qfits_malloc(t->nr * field_size); r = (unsigned char *)array[i]; inbuf = (unsigned char *)(data[i]); /* Copy the data */ if (t->tab_t == QFITS_ASCIITABLE) { /* ASCII table */ for (j=0; jnr; j++) { switch(curr_col->atom_type) { case TFITS_ASCII_TYPE_A : strncpy(field, (char*)inbuf, curr_col->atom_nb); field[curr_col->atom_nb] = '\0'; inbuf += curr_col->atom_nb; break; case TFITS_ASCII_TYPE_D : memset(field, ' ', curr_col->atom_nb); sprintf(field, "%g", ((double*)data[i])[j]); field[curr_col->atom_nb] = '\0'; break; case TFITS_ASCII_TYPE_E : case TFITS_ASCII_TYPE_F : memset(field, ' ', curr_col->atom_nb); sprintf(field, "%f", ((float*)data[i])[j]); field[curr_col->atom_nb] = '\0'; break; case TFITS_ASCII_TYPE_I : memset(field, ' ', curr_col->atom_nb); sprintf(field, "%d", ((int*)data[i])[j]); field[curr_col->atom_nb] = '\0'; break; default: break; } memcpy(r, field, curr_col->atom_nb); r += (curr_col->atom_nb); } } else if (t->tab_t == QFITS_BINTABLE) { /* BINARY table */ for (j=0; jnr; j++) { memcpy(r, inbuf, field_size); inbuf += field_size; r += field_size; } /* Byte swapping needed if on a little-endian machine */ #ifndef WORDS_BIGENDIAN if (curr_col->atom_size > 1) { r = array[i]; for (j=0; jnr * curr_col->atom_nb; j++) { qfits_swap_bytes(r, curr_col->atom_size); r += curr_col->atom_size; } } #endif } else return -1; curr_col++; } /* Write to the outfile */ writt_char = 0; for (i=0; inr; i++) { curr_col = t->col; for (j=0; jnc; j++) { field_size = qfits_table_get_field_size(t->tab_t, curr_col); r = array[j] + field_size * i; line = (char *)qfits_calloc (field_size+1, sizeof (char)); memcpy(line, r, field_size); line[field_size] = '\0'; fwrite(line, 1, field_size, outfile); writt_char += field_size; curr_col++; qfits_free(line); } } /* Complete with blanks to FITS_BLOCK_SIZE characters */ if (writt_char % FITS_BLOCK_SIZE) { nb_blanks = FITS_BLOCK_SIZE - (writt_char%FITS_BLOCK_SIZE); for (i=1; i<=nb_blanks; i++) fwrite(" ", 1, 1, outfile); } /* Free and return */ for(i=0; inc; i++) { if (array[i] != NULL) qfits_free(array[i]); } qfits_free(array); return 0; } /*----------------------------------------------------------------------------*/ /** @brief Get the size in bytes of a field @param type table type @param col a column @return the size */ /*----------------------------------------------------------------------------*/ static int qfits_table_get_field_size( int type, const qfits_col * col) { int field_size; switch (type) { case QFITS_BINTABLE: field_size = col->atom_nb * col->atom_size; break; case QFITS_ASCIITABLE: field_size = col->atom_nb; break; default: qfits_warning("unrecognized table type"); field_size = -1; } return field_size; }