示例#1
0
void plot_quad_xy(cairo_t* cairo, double* quadxy, int dimquads) {
	int k;
	double cx, cy;
	double theta[DQMAX];
	int* perm;

	cx = cy = 0.0;
	for (k=0; k<dimquads; k++) {
		cx += quadxy[2*k+0];
		cy += quadxy[2*k+1];
	}
	cx /= dimquads;
	cy /= dimquads;

	for (k=0; k<dimquads; k++)
		theta[k] = atan2(quadxy[2*k+1] - cy, quadxy[2*k+0] - cx);
	perm = permuted_sort(theta, sizeof(double), compare_doubles_asc, NULL, dimquads);
	for (k=0; k<dimquads; k++) {
		double px,py;
		px = quadxy[2 * perm[k] + 0];
		py = quadxy[2 * perm[k] + 1];
		if (k == 0) {
			cairo_move_to(cairo, px, py);
		} else {
			cairo_line_to(cairo, px, py);
		}
	}
	free(perm);
	cairo_close_path(cairo);
}
示例#2
0
static anbool find_stars(hpquads_t* me, double radius2, int R) {
	int d, j, N;
	int destind;
	double centre[3];
	int* perm;

	healpix_to_xyzarr(me->hp, me->Nside, 0.5, 0.5, centre);
	me->res = kdtree_rangesearch_options_reuse(me->starkd->tree, me->res,
											   centre, radius2, KD_OPTIONS_RETURN_POINTS);

	// here we could check whether stars are in the box defined by the
	// healpix boundaries plus quad scale, rather than just the circle
	// containing that box.

	N = me->res->nres;
	me->Nstars = N;
	if (N < me->dimquads)
		return FALSE;

	// FIXME -- could merge this step with the sorting step...

	// remove stars that have been used up.
	if (R) {
		destind = 0;
		for (j=0; j<N; j++) {
			if (me->nuses[me->res->inds[j]] >= R)
				continue;
			me->res->inds[destind] = me->res->inds[j];
			for (d=0; d<3; d++)
				me->res->results.d[destind*3+d] = me->res->results.d[j*3+d];
			destind++;
		}
		N = destind;
		if (N < me->dimquads)
			return FALSE;
	}

	// sort the stars in increasing order of index - assume
	// that this corresponds to decreasing order of brightness.

	// UNLESS another sorting is provided!

	if (me->sort_data && me->sort_func && me->sort_size) {
		/*
		 Two levels of indirection here!

		 me->res->inds are indices into the "sort_data" array (since kdtree is assumed to be un-permuted)

		 We want to produce "perm", which permutes me->res->inds to make sort_data sorted;
		 need to do this because we also want to permute results.d.

		 Alternatively, we could re-fetch the results.d ...
		 */
		int k;
		char* tempdata = malloc(me->sort_size * N);
		for (k=0; k<N; k++)
			memcpy(tempdata + k*me->sort_size,
				   ((char*)me->sort_data) + me->sort_size * me->res->inds[k],
				   me->sort_size);
		perm = permuted_sort(tempdata, me->sort_size, me->sort_func, NULL, N);
		free(tempdata);

	} else {
		// find permutation that sorts by index...
		perm = permuted_sort(me->res->inds, sizeof(int), compare_ints_asc, NULL, N);
	}
	// apply the permutation...
	permutation_apply(perm, N, me->res->inds, me->res->inds, sizeof(int));
	permutation_apply(perm, N, me->res->results.d, me->res->results.d, 3 * sizeof(double));

	free(perm);

	me->inds = (int*)me->res->inds;
	me->stars = me->res->results.d;
	me->Nstars = N;

	return TRUE;
}
int uniformize_catalog(fitstable_t* intable, fitstable_t* outtable,
					   const char* racol, const char* deccol,
					   const char* sortcol, anbool sort_ascending,
					   double sort_min_cut,
					   // ?  Or do this cut in a separate process?
					   int bighp, int bignside,
					   int nmargin,
					   // uniformization nside.
					   int Nside,
					   double dedup_radius,
					   int nsweeps,
					   char** args, int argc) {
	anbool allsky;
	intmap_t* starlists;
	int NHP;
	anbool dense = FALSE;
	double dedupr2 = 0.0;
	tfits_type dubl;
	int N;
	int* inorder = NULL;
	int* outorder = NULL;
	int outi;
	double *ra = NULL, *dec = NULL;
	il* myhps = NULL;
	int i,j,k;
	int nkeep = nsweeps;
	int noob = 0;
	int ndup = 0;
	struct oh_token token;
	int* npersweep = NULL;
	qfits_header* outhdr = NULL;
	double *sortval = NULL;

	if (bignside == 0)
		bignside = 1;
	allsky = (bighp == -1);

    if (Nside % bignside) {
        ERROR("Fine healpixelization Nside must be a multiple of the coarse healpixelization Nside");
        return -1;
    }
	if (Nside > HP_MAX_INT_NSIDE) {
		ERROR("Error: maximum healpix Nside = %i", HP_MAX_INT_NSIDE);
		return -1;
	}

	NHP = 12 * Nside * Nside;
	logverb("Healpix Nside: %i, # healpixes on the whole sky: %i\n", Nside, NHP);
	if (!allsky) {
		logverb("Creating index for healpix %i, nside %i\n", bighp, bignside);
		logverb("Number of healpixes: %i\n", ((Nside/bignside)*(Nside/bignside)));
	}
	logverb("Healpix side length: %g arcmin.\n", healpix_side_length_arcmin(Nside));

	dubl = fitscolumn_double_type();
	if (!racol)
		racol = "RA";
	ra = fitstable_read_column(intable, racol, dubl);
	if (!ra) {
		ERROR("Failed to find RA column (%s) in table", racol);
		return -1;
	}
	if (!deccol)
		deccol = "DEC";
	dec = fitstable_read_column(intable, deccol, dubl);
	if (!dec) {
		ERROR("Failed to find DEC column (%s) in table", deccol);
		free(ra);
		return -1;
	}

	N = fitstable_nrows(intable);
	logverb("Have %i objects\n", N);

	// FIXME -- argsort and seek around the input table, and append to
	// starlists in order; OR read from the input table in sequence and
	// sort in the starlists?
	if (sortcol) {
		logverb("Sorting by %s...\n", sortcol);
		sortval = fitstable_read_column(intable, sortcol, dubl);
		if (!sortval) {
			ERROR("Failed to read sorting column \"%s\"", sortcol);
			free(ra);
			free(dec);
			return -1;
		}
		inorder = permuted_sort(sortval, sizeof(double),
								sort_ascending ? compare_doubles_asc : compare_doubles_desc,
								NULL, N);
		if (sort_min_cut > -HUGE_VAL) {
			logverb("Cutting to %s > %g...\n", sortcol, sort_min_cut);
			// Cut objects with sortval < sort_min_cut.
			if (sort_ascending) {
				// skipped objects are at the front -- find the first obj
				// to keep
				for (i=0; i<N; i++)
					if (sortval[inorder[i]] > sort_min_cut)
						break;
				// move the "inorder" indices down.
				if (i)
					memmove(inorder, inorder+i, (N-i)*sizeof(int));
				N -= i;
			} else {
				// skipped objects are at the end -- find the last obj to keep.
				for (i=N-1; i>=0; i--)
					if (sortval[inorder[i]] > sort_min_cut)
						break;
				N = i+1;
			}
			logverb("Cut to %i objects\n", N);
		}
		//free(sortval);
	}

	token.nside = bignside;
	token.finenside = Nside;
	token.hp = bighp;

	if (!allsky && nmargin) {
		int bigbighp, bighpx, bighpy;
		//int ninside;
		il* seeds = il_new(256);
		logverb("Finding healpixes in range...\n");
        healpix_decompose_xy(bighp, &bigbighp, &bighpx, &bighpy, bignside);
		//ninside = (Nside/bignside)*(Nside/bignside);
		// Prime the queue with the fine healpixes that are on the
		// boundary of the big healpix.
		for (i=0; i<((Nside / bignside) - 1); i++) {
			// add (i,0), (i,max), (0,i), and (0,max) healpixes
            int xx = i + bighpx * (Nside / bignside);
            int yy = i + bighpy * (Nside / bignside);
            int y0 =     bighpy * (Nside / bignside);
			// -1 prevents us from double-adding the corners.
            int y1 =(1 + bighpy)* (Nside / bignside) - 1;
            int x0 =     bighpx * (Nside / bignside);
            int x1 =(1 + bighpx)* (Nside / bignside) - 1;
            assert(xx < Nside);
            assert(yy < Nside);
            assert(x0 < Nside);
            assert(x1 < Nside);
            assert(y0 < Nside);
            assert(y1 < Nside);
			il_append(seeds, healpix_compose_xy(bigbighp, xx, y0, Nside));
			il_append(seeds, healpix_compose_xy(bigbighp, xx, y1, Nside));
			il_append(seeds, healpix_compose_xy(bigbighp, x0, yy, Nside));
			il_append(seeds, healpix_compose_xy(bigbighp, x1, yy, Nside));
		}
        logmsg("Number of boundary healpixes: %zu (Nside/bignside = %i)\n", il_size(seeds), Nside/bignside);

		myhps = healpix_region_search(-1, seeds, Nside, NULL, NULL,
									  outside_healpix, &token, nmargin);
		logmsg("Number of margin healpixes: %zu\n", il_size(myhps));
		il_free(seeds);

		il_sort(myhps, TRUE);
		// DEBUG
		il_check_consistency(myhps);
		il_check_sorted_ascending(myhps, TRUE);
	}

	dedupr2 = arcsec2distsq(dedup_radius);
	starlists = intmap_new(sizeof(int32_t), nkeep, 0, dense);

	logverb("Placing stars in grid cells...\n");
	for (i=0; i<N; i++) {
		int hp;
		bl* lst;
		int32_t j32;
		anbool oob;
		if (inorder) {
			j = inorder[i];
			//printf("Placing star %i (%i): sort value %s = %g, RA,Dec=%g,%g\n", i, j, sortcol, sortval[j], ra[j], dec[j]);
		} else
			j = i;
		
		hp = radecdegtohealpix(ra[j], dec[j], Nside);
		//printf("HP %i\n", hp);
		// in bounds?
		oob = FALSE;
		if (myhps) {
			oob = (outside_healpix(hp, &token) && !il_sorted_contains(myhps, hp));
		} else if (!allsky) {
			oob = (outside_healpix(hp, &token));
		}
		if (oob) {
			//printf("out of bounds.\n");
			noob++;
			continue;
		}

		lst = intmap_find(starlists, hp, TRUE);
		/*
		 printf("list has %i existing entries.\n", bl_size(lst));
		 for (k=0; k<bl_size(lst); k++) {
		 bl_get(lst, k, &j32);
		 printf("  %i: index %i, %s = %g\n", k, j32, sortcol, sortval[j32]);
		 }
		 */

		// is this list full?
		if (nkeep && (bl_size(lst) >= nkeep)) {
			// Here we assume we're working in sorted order: once the list is full we're done.
			//printf("Skipping: list is full.\n");
			continue;
		}

		if ((dedupr2 > 0.0) &&
			is_duplicate(hp, ra[j], dec[j], Nside, starlists, ra, dec, dedupr2)) {
			//printf("Skipping: duplicate\n");
			ndup++;
			continue;
		}

		// Add the new star (by index)
		j32 = j;
		bl_append(lst, &j32);
	}
	logverb("%i outside the healpix\n", noob);
	logverb("%i duplicates\n", ndup);

	il_free(myhps);
	myhps = NULL;
	free(inorder);
	inorder = NULL;
	free(ra);
	ra = NULL;
	free(dec);
	dec = NULL;

	outorder = malloc(N * sizeof(int));
	outi = 0;

	npersweep = calloc(nsweeps, sizeof(int));

	for (k=0; k<nsweeps; k++) {
		int starti = outi;
		int32_t j32;
		for (i=0;; i++) {
			bl* lst;
			int hp;
			if (!intmap_get_entry(starlists, i, &hp, &lst))
				break;
			if (bl_size(lst) <= k)
				continue;
			bl_get(lst, k, &j32);
			outorder[outi] = j32;
			//printf("sweep %i, cell #%i, hp %i, star %i, %s = %g\n", k, i, hp, j32, sortcol, sortval[j32]);
			outi++;
		}
		logmsg("Sweep %i: %i stars\n", k+1, outi - starti);
		npersweep[k] = outi - starti;

		if (sortcol) {
			// Re-sort within this sweep.
			permuted_sort(sortval, sizeof(double),
						  sort_ascending ? compare_doubles_asc : compare_doubles_desc,
						  outorder + starti, npersweep[k]);
			/*
			 for (i=0; i<npersweep[k]; i++) {
			 printf("  within sweep %i: star %i, j=%i, %s=%g\n",
			 k, i, outorder[starti + i], sortcol, sortval[outorder[starti + i]]);
			 }
			 */
		}

	}
	intmap_free(starlists);
	starlists = NULL;

	//////
	free(sortval);
	sortval = NULL;

	logmsg("Total: %i stars\n", outi);
	N = outi;

	outhdr = fitstable_get_primary_header(outtable);
    if (allsky)
        qfits_header_add(outhdr, "ALLSKY", "T", "All-sky catalog.", NULL);
    BOILERPLATE_ADD_FITS_HEADERS(outhdr);
    qfits_header_add(outhdr, "HISTORY", "This file was generated by the command-line:", NULL, NULL);
    fits_add_args(outhdr, args, argc);
    qfits_header_add(outhdr, "HISTORY", "(end of command line)", NULL, NULL);
	fits_add_long_history(outhdr, "uniformize-catalog args:");
	fits_add_long_history(outhdr, "  RA,Dec columns: %s,%s", racol, deccol);
	fits_add_long_history(outhdr, "  sort column: %s", sortcol);
	fits_add_long_history(outhdr, "  sort direction: %s", sort_ascending ? "ascending" : "descending");
	if (sort_ascending)
		fits_add_long_history(outhdr, "    (ie, for mag-like sort columns)");
	else
		fits_add_long_history(outhdr, "    (ie, for flux-like sort columns)");
	fits_add_long_history(outhdr, "  uniformization nside: %i", Nside);
	fits_add_long_history(outhdr, "    (ie, side length ~ %g arcmin)", healpix_side_length_arcmin(Nside));
	fits_add_long_history(outhdr, "  deduplication scale: %g arcsec", dedup_radius);
	fits_add_long_history(outhdr, "  number of sweeps: %i", nsweeps);

    fits_header_add_int(outhdr, "NSTARS", N, "Number of stars.");
    fits_header_add_int(outhdr, "HEALPIX", bighp, "Healpix covered by this catalog, with Nside=HPNSIDE");
    fits_header_add_int(outhdr, "HPNSIDE", bignside, "Nside of HEALPIX.");
	fits_header_add_int(outhdr, "CUTNSIDE", Nside, "uniformization scale (healpix nside)");
	fits_header_add_int(outhdr, "CUTMARG", nmargin, "margin size, in healpixels");
	//qfits_header_add(outhdr, "CUTBAND", cutband, "band on which the cut was made", NULL);
	fits_header_add_double(outhdr, "CUTDEDUP", dedup_radius, "deduplication radius [arcsec]");
	fits_header_add_int(outhdr, "CUTNSWEP", nsweeps, "number of sweeps");
	//fits_header_add_double(outhdr, "CUTMINMG", minmag, "minimum magnitude");
	//fits_header_add_double(outhdr, "CUTMAXMG", maxmag, "maximum magnitude");
	for (k=0; k<nsweeps; k++) {
		char key[64];
		sprintf(key, "SWEEP%i", (k+1));
        fits_header_add_int(outhdr, key, npersweep[k], "# stars added");
	}
	free(npersweep);

	if (fitstable_write_primary_header(outtable)) {
		ERROR("Failed to write primary header");
		return -1;
	}

	// Write output.
	fitstable_add_fits_columns_as_struct2(intable, outtable);
	if (fitstable_write_header(outtable)) {
		ERROR("Failed to write output table header");
		return -1;
	}
	logmsg("Writing output...\n");
	logverb("Row size: %i\n", fitstable_row_size(intable));
	if (fitstable_copy_rows_data(intable, outorder, N, outtable)) {
		ERROR("Failed to copy rows from input table to output");
		return -1;
	}
	if (fitstable_fix_header(outtable)) {
		ERROR("Failed to fix output table header");
		return -1;
	}
	free(outorder);
	return 0;
}
示例#4
0
int resort_xylist(const char* infn, const char* outfn,
                  const char* fluxcol, const char* backcol,
                  anbool ascending) {
	FILE* fin = NULL;
	FILE* fout = NULL;
    double *flux = NULL, *back = NULL;
    int *perm1 = NULL, *perm2 = NULL;
    anbool *used = NULL;
    int start, size, nextens, ext;
    int (*compare)(const void*, const void*);
    fitstable_t* tab = NULL;
    anqfits_t* anq = NULL;

    if (ascending)
        compare = compare_doubles_asc;
    else
        compare = compare_doubles_desc;

    if (!fluxcol)
        fluxcol = "FLUX";
    if (!backcol)
        backcol = "BACKGROUND";

    fin = fopen(infn, "rb");
    if (!fin) {
        SYSERROR("Failed to open input file %s", infn);
        return -1;
    }

    fout = fopen(outfn, "wb");
    if (!fout) {
        SYSERROR("Failed to open output file %s", outfn);
        goto bailout;
    }

	// copy the main header exactly.
    anq = anqfits_open(infn);
    if (!anq) {
        ERROR("Failed to open file \"%s\"", infn);
        goto bailout;
    }
    start = anqfits_header_start(anq, 0);
    size  = anqfits_header_size (anq, 0);

    if (pipe_file_offset(fin, start, size, fout)) {
        ERROR("Failed to copy primary FITS header.");
        goto bailout;
    }

	nextens = anqfits_n_ext(anq);

    tab = fitstable_open(infn);
    if (!tab) {
        ERROR("Failed to open FITS table in file %s", infn);
        goto bailout;
    }

	for (ext=1; ext<nextens; ext++) {
		int hdrstart, hdrsize, datstart;
		int i, N;
        int rowsize;

        hdrstart = anqfits_header_start(anq, ext);
        hdrsize  = anqfits_header_size (anq, ext);
        datstart = anqfits_data_start  (anq, ext);

        if (!anqfits_is_table(anq, ext)) {
            ERROR("Extention %i isn't a table. Skipping", ext);
			continue;
		}
        // Copy the header as-is.
        if (pipe_file_offset(fin, hdrstart, hdrsize, fout)) {
            ERROR("Failed to copy the header of extension %i", ext);
			goto bailout;
        }

        if (fitstable_read_extension(tab, ext)) {
            ERROR("Failed to read FITS table from extension %i", ext);
            goto bailout;
        }
        rowsize = fitstable_row_size(tab);

        // read FLUX column as doubles.
        flux = fitstable_read_column(tab, fluxcol, TFITS_BIN_TYPE_D);
        if (!flux) {
            ERROR("Failed to read FLUX column from extension %i", ext);
            goto bailout;
        }
        // BACKGROUND
        back = fitstable_read_column(tab, backcol, TFITS_BIN_TYPE_D);
        if (!back) {
            ERROR("Failed to read BACKGROUND column from extension %i", ext);
            goto bailout;
        }

		debug("First 10 rows of input table:\n");
		for (i=0; i<10; i++)
			debug("flux %g, background %g\n", flux[i], back[i]);

        N = fitstable_nrows(tab);

        // set back = flux + back (ie, non-background-subtracted flux)
		for (i=0; i<N; i++)
            back[i] += flux[i];

        // Sort by flux...
		perm1 = permuted_sort(flux, sizeof(double), compare, NULL, N);

        // Sort by non-background-subtracted flux...
		perm2 = permuted_sort(back, sizeof(double), compare, NULL, N);

        used = malloc(N * sizeof(anbool));
        memset(used, 0, N * sizeof(anbool));

		// Check sort...
        for (i=0; i<N-1; i++) {
			if (ascending) {
				assert(flux[perm1[i]] <= flux[perm1[i+1]]);
				assert(back[perm2[i]] <= back[perm2[i+1]]);
			} else {
				assert(flux[perm1[i]] >= flux[perm1[i+1]]);
				assert(back[perm2[i]] >= back[perm2[i+1]]);
			}
		}

        for (i=0; i<N; i++) {
            int j;
            int inds[] = { perm1[i], perm2[i] };
            for (j=0; j<2; j++) {
                int index = inds[j];
				assert(index < N);
                if (used[index])
                    continue;
                used[index] = TRUE;
				debug("adding index %i: %s %g\n", index, j==0 ? "flux" : "bgsub", j==0 ? flux[index] : back[index]);
                if (pipe_file_offset(fin, datstart + index * rowsize, rowsize, fout)) {
                    ERROR("Failed to copy row %i", index);
                    goto bailout;
                }
            }
        }

        for (i=0; i<N; i++)
			assert(used[i]);

		if (fits_pad_file(fout)) {
			ERROR("Failed to add padding to extension %i", ext);
            goto bailout;
		}

        free(flux);
        flux = NULL;
        free(back);
        back = NULL;
        free(perm1);
        perm1 = NULL;
        free(perm2);
        perm2 = NULL;
        free(used);
        used = NULL;
    }

    fitstable_close(tab);
    tab = NULL;

	if (fclose(fout)) {
		SYSERROR("Failed to close output file %s", outfn);
        return -1;
    }
	fclose(fin);
    return 0;

 bailout:
    if (tab)
        fitstable_close(tab);
    if (fout)
        fclose(fout);
    if (fin)
        fclose(fin);
    free(flux);
    free(back);
    free(perm1);
    free(perm2);
    free(used);
	return -1;
}
示例#5
0
int tabsort(const char* infn, const char* outfn, const char* colname,
            int descending) {
	FILE* fin;
	FILE* fout;
	int ext, nextens;
	off_t start, size;
    void* data = NULL;
    int* perm = NULL;
    unsigned char* map = NULL;
    size_t mapsize = 0;
    anqfits_t* anq = NULL;

    fin = fopen(infn, "rb");
    if (!fin) {
        SYSERROR("Failed to open input file %s", infn);
        return -1;
    }

    fout = fopen(outfn, "wb");
    if (!fout) {
        SYSERROR("Failed to open output file %s", outfn);
        goto bailout;
    }

	// copy the main header exactly.
    anq = anqfits_open(infn);
    if (!anq) {
        ERROR("Failed to open \"%s\"", infn);
        goto bailout;
    }
    start = anqfits_header_start(anq, 0);
    size  = anqfits_header_size (anq, 0);
    if (pipe_file_offset(fin, start, size, fout)) {
        ERROR("Failed to copy primary FITS header.");
        goto bailout;
    }

	nextens = anqfits_n_ext(anq);
    //logverb("Sorting %i extensions.\n", nextens);
	for (ext=1; ext<nextens; ext++) {
		int c;
		qfits_table* table;
		qfits_col* col;
		int mgap;
		off_t mstart;
		size_t msize;
		int atomsize;
		int (*sort_func)(const void*, const void*);
		unsigned char* tabledata;
		unsigned char* tablehdr;
		off_t hdrstart, hdrsize, datsize, datstart;
		int i;

        hdrstart = anqfits_header_start(anq, ext);
        hdrsize  = anqfits_header_size (anq, ext);
        datstart = anqfits_data_start  (anq, ext);
        datsize  = anqfits_data_size   (anq, ext);
		if (!anqfits_is_table(anq, ext)) {
            ERROR("Extension %i isn't a table. Skipping.\n", ext);
			continue;
		}
		table = anqfits_get_table(anq, ext);
		if (!table) {
			ERROR("Failed to open table: file %s, extension %i. Skipping.", infn, ext);
			continue;
		}
		c = fits_find_column(table, colname);
		if (c == -1) {
			ERROR("Couldn't find column named \"%s\" in extension %i.  Skipping.", colname, ext);
			continue;
		}
		col = table->col + c;
		switch (col->atom_type) {
		case TFITS_BIN_TYPE_D:
			data = realloc(data, table->nr * sizeof(double));
			if (descending)
				sort_func = compare_doubles_desc;
			else
				sort_func = compare_doubles_asc;
			break;
		case TFITS_BIN_TYPE_E:
			data = realloc(data, table->nr * sizeof(float));
			if (descending)
				sort_func = compare_floats_desc;
			else
				sort_func = compare_floats_asc;
			break;
        case TFITS_BIN_TYPE_K:
            data = realloc(data, table->nr * sizeof(int64_t));
			if (descending)
				sort_func = compare_int64_desc;
			else
				sort_func = compare_int64_asc;
			break;

		default:
			ERROR("Column %s is neither FITS type D, E, nor K.  Skipping.", colname);
			continue;
		}

        // Grab the sort column.
		atomsize = fits_get_atom_size(col->atom_type);
        printf("Reading sort column \"%s\"\n", colname);
		qfits_query_column_seq_to_array(table, c, 0, table->nr, data, atomsize);
        // Sort it.
        printf("Sorting sort column\n");
		perm = permuted_sort(data, atomsize, sort_func, NULL, table->nr);

        // mmap the input file.
        printf("mmapping input file\n");
		start = hdrstart;
		size = hdrsize + datsize;
		get_mmap_size(start, size, &mstart, &msize, &mgap);
		mapsize = msize;
		map = mmap(NULL, mapsize, PROT_READ, MAP_SHARED, fileno(fin), mstart);
		if (map == MAP_FAILED) {
			SYSERROR("Failed to mmap input file %s", infn);
            map = NULL;
            goto bailout;
		}
		tabledata = map + (off_t)mgap + (datstart - hdrstart);
		tablehdr  = map + (off_t)mgap;

        // Copy the table header without change.
        printf("Copying table header.\n");
		if (fwrite(tablehdr, 1, hdrsize, fout) != hdrsize) {
			SYSERROR("Failed to write FITS table header");
            goto bailout;
		}

		for (i=0; i<table->nr; i++) {
			unsigned char* rowptr;
            if (i % 100000 == 0)
                printf("Writing row %i\n", i);
			rowptr = tabledata + (off_t)(perm[i]) * (off_t)table->tab_w;
			if (fwrite(rowptr, 1, table->tab_w, fout) != table->tab_w) {
				SYSERROR("Failed to write FITS table row");
                goto bailout;
			}
		}

		munmap(map, mapsize);
        map = NULL;
		free(perm);
        perm = NULL;

		if (fits_pad_file(fout)) {
			ERROR("Failed to add padding to extension %i", ext);
            goto bailout;
		}

        qfits_table_close(table);
	}
	free(data);

	if (fclose(fout)) {
		SYSERROR("Error closing output file");
        fout = NULL;
        goto bailout;
	}
	fclose(fin);
    anqfits_close(anq);
    printf("Done\n");
	return 0;

 bailout:
    free(data);
    free(perm);
    if (fout)
        fclose(fout);
    fclose(fin);
    if (map)
        munmap(map, mapsize);
    return -1;
}