diff options
Diffstat (limited to 'astro/fits')
| -rwxr-xr-x | astro/fits/merge_fits.py | 234 |
1 files changed, 234 insertions, 0 deletions
diff --git a/astro/fits/merge_fits.py b/astro/fits/merge_fits.py new file mode 100755 index 0000000..e014c69 --- /dev/null +++ b/astro/fits/merge_fits.py @@ -0,0 +1,234 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +# +# Aaron LI +# 2015/06/16 +# +# Changelogs: +# 0.3.0, 2015/06/17, Aaron LI +# * added argument '-c/--columns' to specify columns to be merged +# * added argument 'columns' to function 'merge2fits()' +# 0.2.0, 2015/06/17, Aaron LI +# * added function 'del_key_startswith()' to delete header keywords, +# and the deletion must be repeated until the header length does not +# decrease any more +# * ignore the header of the second FITS file to avoid keyword conflictions +# +# BUGS: +# * astropy.io.fits may have bug with header keywords deletion +# +# TODO: +# * to support image FITS merge +# * to allow specify column list to be merged +# + +""" +Merge several (>=2) of FITS file. + +By default the *first* extend tables are merged and write out to a new +FITS file containing the *common* columns. If the data types of the +columns of each FITS table do not match, then the data type of the column +of the *first* FITS table is used, and other columns are coerced. + +If the FITS files have only *1* HDU (i.e., the Primary HDU), then data of +these HDU's are summed up to make up the output FITS file (an image), +on conditional that the shapes of all these HDU's are the same. +""" + +__version__ = "0.3.0" +__date__ = "2015/06/17" + +# default blockname to be merged +BLOCKNAME_DFT = "EVENTS" + +DEBUG = True + +import sys +import argparse +import re + +import numpy as np +try: + from astropy.io import fits +except ImportError: + try: + import pyfits as fits + except ImportError: + raise ImportError("cannot import 'astropy.io.fits' or 'pyfits'") + + +def merge2fits(file1, file2, block1=1, block2=1, columns=None): + """ + Merge *two* FITS files of the given blocks (extension table), + and return the merged FITS object. + + TODO: + * log history to header + + Arguments: + file1, file2: input two FITS files + block1, block2: table number or table name to be merged + columns: the columns to be merged; by default to merge the + common columns + + Return: + the merged FITS object + """ + # open file if provide filename + if isinstance(file1, str): + file1 = fits.open(file1) + if isinstance(file2, str): + file2 = fits.open(file2) + # if has only *1* HDU => image + if len(file1) == 1: + block1 = 0 + if len(file2) == 1: + block2 = 0 + if block1 == 0 or block2 == 0: + # TODO + raise NotImplementedError("image FITS merge currently not supported!") + # get table to be merged + table1 = file1[block1] + table2 = file2[block2] + # create column names to be merged + # get names of all columns (convert to upper case) + colnames1 = [col.name.upper() for col in table1.columns] + colnames2 = [col.name.upper() for col in table2.columns] + colnames_common = list(set(colnames1).intersection(set(colnames2))) + # sort the common column names acoording original column orders + colnames_common.sort(key = lambda x: colnames1.index(x)) + if columns is not None: + if isinstance(columns, list): + columnlist = list(map(str.upper, columns)) + else: + columnlist = list(columns.upper()) + # check the specified columns whether in the above colnames_common + for name in columnlist: + if name not in colnames_common: + raise ValueError("column '%s' not found in both files" % name) + # use the specified columns + colnames_common = columnlist + # "STATUS" columns don't have equal-length format, so remove it + if "STATUS" in colnames_common: + colnames_common.remove("STATUS") + if DEBUG: + print("DEBUG: columns to merge: ", colnames_common, file=sys.stderr) + # filter out the common columns + nrow1 = table1.data.shape[0] + nrow2 = table2.data.shape[0] + hdu_merged = fits.BinTableHDU.from_columns( + fits.ColDefs([table1.columns[name] for name in colnames_common]), + nrows=nrow1+nrow2) + for name in colnames_common: + if DEBUG: + print("DEBUG: merging column: ", name, file=sys.stderr) + dtype = hdu_merged.columns[name].array.dtype + hdu_merged.columns[name].array[nrow1:] = \ + table2.columns[name].array.astype(dtype) + # process headers, based on the header of the first FITS file + # DO NOT strip the base header, in order to keep the position of + # XTENSION/BITPIX/NAXIS/NAXIS1/NAXIS2/PCOUNT/GCOUNT/TFIELDS keywords. + header = table1.header.copy() # do not strip + # IGNORE the header of the second FITS file to avoid keyword conflictions. + #header2 = table2.header.copy(strip=True) + ## merge two headers; COMMENT and HISTORY needs special handle + #for comment in header2["COMMENT"]: + # header.add_comment(comment) + #for history in header2["HISTORY"]: + # header.add_history(history) + #if "COMMENT" in header2: + # del header2["COMMENT"] + #if "HISTORY" in header2: + # del header2["HISTORY"] + #if "" in header2: + # del header2[""] + #header.update(header2) + # remove the original TLMIN??/TLMAX??/TTYPE??/TFORM??/TUNIT?? keywords + del_key_startswith(header, + startswith=["TLMIN", "TLMAX", "TTYPE", "TFORM", "TUNIT"], + lastlength=len(header)) + # update with new TLMIN??/TLMAX??/TTYPE??/TFORM??/TUNIT?? keywords + header.update(hdu_merged.header) + hdu_merged.header = header + # copy PrimaryHDU from first FITS + primary_hdu = file1[0].copy() + # make HDUList and return + return fits.HDUList([primary_hdu, hdu_merged]) + + +def del_key_startswith(header, startswith, lastlength=0): + """ + Delete the keys which start with the specified strings. + + Arguments: + header: FITS table header + startswith: a list of strings; If a key starts with any + of these strings, then the key-value pair is removed. + + XXX: the deletion must be repeated several times until the + length of the header does not decrease any more. + (This may be a bug related to the astropy.io.fits???) + """ + if not isinstance(startswith, list): + startswith = list(startswith) + re_key = re.compile(r"^(%s)" % "|".join(startswith), re.I) + for k in header.keys(): + if re_key.match(k): + del header[k] + curlength = len(header) + if lastlength == curlength: + return + else: + # recursively continue deletion + if DEBUG: + print("DEBUG: recursively continue header keywords deleteion", + file=sys.stderr) + del_key_startswith(header, startswith, curlength) + + +def get_filename_blockname(pstr): + """ + Separate privided 'pstr' (parameter string) into filename and + blockname. If does not have a blockname, then the default + blockname returned. + """ + try: + filename, blockname = re.sub(r"[\[\]]", " ", pstr).split() + except ValueError: + filename = pstr + blockname = BLOCKNAME_DFT + return (filename, blockname) + + +def main(): + parser = argparse.ArgumentParser( + description="Merge several FITS files with the common columns.") + parser.add_argument("-V", "--version", action="version", + version="%(prog)s " + "%s (%s)" % (__version__, __date__)) + parser.add_argument("infile1", help="input FITS file 1; " + \ + "The blockname can be appended, e.g., infile1.fits[EVENTS]") + parser.add_argument("infile2", nargs="+", + help="input FITS file 2 and more") + parser.add_argument("outfile", help="merged output file") + parser.add_argument("-c", "--columns", dest="columns", + help="list of columns to be merged (comma separated)") + parser.add_argument("-C", "--clobber", dest="clobber", + action="store_true", help="overwrite output file if exists") + args = parser.parse_args() + if DEBUG: + print("DEBUG: infile2: ", args.infile2, file=sys.stderr) + + if args.columns: + columns = args.columns.upper().replace(",", " ").split() + file1, block1 = get_filename_blockname(args.infile1) + merged_fits = fits.open(file1) + for fitsfile in args.infile2: + # split filename and block name + file2, block2 = get_filename_blockname(fitsfile) + merged_fits = merge2fits(merged_fits, file2, block1, block2, columns) + merged_fits.writeto(args.outfile, checksum=True, clobber=args.clobber) + + +if __name__ == "__main__": + main() + |