Move fits/merge_fits.py to fitstable_merge.py

1 files changed, 0 insertions, 234 deletions

diff --git a/astro/fits/merge_fits.py b/astro/fits/merge_fits.py
deleted file mode 100755
index e014c69..0000000
--- a/astro/fits/merge_fits.py
+++ /dev/null
@@ -1,234 +0,0 @@
-#!/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()
-