#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Chop chunks or crystals from one or both ends of a stream
#
# Copyright © 2014-2017 Deutsches Elektronen-Synchrotron DESY,
#                       a research centre of the Helmholtz Association.
#
# Author:
#    2014-2017 Thomas White <taw@physics.org>
#

import sys
import optparse
from collections import deque

def count_crystals(f, g, start_after, stop_after):

    n_crystals_seen = 0
    n_crystals_written = 0
    in_crystal = 0
    in_header = 1
    in_chunk_prelim = 0
    need_end_chunk = 0

    chunk_so_far = deque()

    while True:

        fline = f.readline()
        if not fline:
            break

        if fline.find("Begin chunk") != -1:
            in_header = 0
            in_chunk_prelim = 1
            chunk_so_far.clear()

        if in_chunk_prelim:
            chunk_so_far.append(fline)

        if fline.find("End chunk") != -1:
            in_chunk = 0
            if need_end_chunk:
                g.write(fline)
                need_end_chunk = 0
            if (stop_after != 0) and (n_crystals_written == stop_after):
                break

        if in_crystal or in_header:
            g.write(fline)

        if fline.find("Begin crystal") != -1:
            in_chunk_prelim = 0
            if ( (n_crystals_seen >= start_after)
             and ((stop_after == 0) or (n_crystals_written < stop_after)) ):
                in_crystal = 1
                for line in chunk_so_far:
                    g.write(line)
                chunk_so_far.clear()

        if fline.find("End crystal") != -1:
            n_crystals_seen += 1
            if in_crystal:
                n_crystals_written += 1
                in_crystal = 0
                need_end_chunk = 1

    print("Wrote {} crystals to {}".format(n_crystals_written, opt.ofn))

def count_chunks(f, g, start_after, stop_after):
    n_chunks_seen = 0
    n_chunks_written = 0
    in_chunk = 0
    in_header = 1
    while True:

        fline = f.readline()
        if not fline:
            break

        if fline.find("Begin chunk") != -1:
            in_header = 0
            if ( n_chunks_seen >= start_after ):
                in_chunk = 1

        if in_chunk or in_header:
            g.write(fline)

        if fline.find("End chunk") != -1:
            n_chunks_seen += 1
            if in_chunk:
                n_chunks_written += 1
                in_chunk = 0
                if n_chunks_written == stop_after:
                    break

    print("Wrote {} chunks to {}".format(n_chunks_written, opt.ofn))

op = optparse.OptionParser()
op.add_option('', '--input', action='store', type='string', dest='ifn',
              help="Input stream")
op.add_option('', '--output', action='store', type='string', dest='ofn',
              help="Output stream")
op.add_option('', '--start-after', action='store', type='int', dest='start',
              help="Start after this many crystals", default=0)
op.add_option('', '--stop-after', action='store', type='int', dest='stop',
              help="Stop after this many crystals (0=never stop)", default=0)
op.add_option('', '--chunks', action='store_true', dest='chunks',
              help="Count chunks instead of crystals")
opt,arg = op.parse_args(sys.argv)

if not (opt.ifn and opt.ofn):
    print("You need at least --input and --output")
    exit(1)

if opt.ifn == "-":
    f = sys.stdin
else:
    f = open(opt.ifn, 'r')

g = open(opt.ofn, 'w')
start_after = opt.start
stop_after = opt.stop

if opt.chunks:
    count_chunks(f, g, start_after, stop_after)
else:
    count_crystals(f, g, start_after, stop_after)

f.close()
g.close()