Source code for pyhetdex.het.ifu_centers
"""Parse and manipulation of the IFU center files with the following structure
::
# HETDEX IFU description file
# $Id: IFUcen_HETDEX.txt 789 2012-08-17 19:52:17Z mxhf $
#
# IFU 00001
#
# Test date: YYYYMMDD
# Total number of dead fibers (T < X %):
#
#
# history
# date author change
# -------------------------
# 20110702 mF created
#
#
# FIBERD FIBERSEP
1.55 2.20
# NFIBX NFIBY
20 23
#
# col 1: fiber ID, starts with 1, IDs 1-246 belong to left unit, 247-492 belong to right unit
# col 2: fiber x position ["]
# col 3: fiber y position ["]
# col 4: target unit spectrograph L=left, R=right
# col 5: target fiber within the spectrograph, fiber numbers start with 1 within each spectrograph
# col 6: relative throughput at fiducial wavelength
#
0001 -19.8000 -19.6876 L 0001 1.000
0002 -17.6000 -19.6876 L 0002 1.000
[...]
0447 17.6000 19.6876 R 0223 1.000
0448 19.8000 19.6876 R 0224 1.000
From the header the ``FIBERD``, ``FIBERSEP``, ``NFIBX`` and ``NFIBY`` are
extracted. The rest of the file is parsed as follow:
* the number of ``L`` or ``R`` are counted;
* the columns number 2, 3, 5 and 6 are stored in dictionaries with the
channels as keys;
* a row is ignored if:
1. it starts with ``#``;
2. the target fiber number is negative or cannot be converted to an
integer (e.g. ``nan``, ``--``);
* if the throughput if a valid fiber is less than ``0.01`` a
:class:`IFUCenterError` is raised as such a fiber should be ignored.
"""
from __future__ import print_function, absolute_import
from collections import defaultdict
import pyhetdex.tools.files.file_tools as ft
[docs]class IFUCenterError(ValueError):
"Exception raised when the IFU center file parsing fails"
pass
[docs]class IFUCenter(object):
"""Parse the IFU center file
Parameters
----------
ifu_center_file : string
file containing the fiber positions in the IFU.
Attributes
----------
filename : string
name of the IFU center file
fiber_d : float
fiber diameter
fiber_sep : float
fiber separation
nfibx, nfiby : int
number of fibers in the x and y directions
xifu, yifu : dictionary of lists
fibers x and y positions per channel
n_fibers : dictionary of int
number of fibers per channel
fib_number : dictionary of lists
fiber number corresponding to positions ``xifu``, ``yifu`` per channel
throughput : dictionary of lists
throughput corresponding to positions ``xifu``, ``yifu`` per channel
Raises
------
IFUCenterError
if it cannot decide whether a fibers must be used or not
"""
def __init__(self, ifu_center_file):
# these constitute the public interface
self.filename = ifu_center_file
self.fiber_d = 0.
self.fiber_sep = 0.
self.nfibx, self.nfiby = 0, 0
self.xifu, self.yifu = defaultdict(list), defaultdict(list)
self.n_fibers = defaultdict(int)
self.fib_number = defaultdict(list)
self.throughput = defaultdict(list)
self._read_ifu(ifu_center_file)
[docs] def _read_ifu(self, ifu_center_file):
"""Read the ifu center file
Parameters
----------
ifu_center_file : string
file containing the fiber number to fiber position mapping
"""
with open(ifu_center_file, 'r') as f:
f = self._read_header(f)
f = self._read_ifu_map(f)
[docs] def _read_ifu_map(self, f):
"""
Parameters
----------
f : file object
file to parse
Returns
-------
f : file object
moved to the next non comment line
"""
for line in f:
if line.startswith('#'):
continue
_x, _y, _channel, _fib_n, _t = line.split()[1:6]
# convert the fiber number to integer. If fails, means that the
# fiber is broken
try:
_fib_n = int(_fib_n)
except ValueError:
continue
if _fib_n > 0:
if float(_t) < 0.01: # zero or less
msg = 'In the fiber mapping file there is at least one'
msg += ' fiber with positive fiber number and 0 throughput'
msg += '. What should I do?'
raise IFUCenterError(msg)
else:
self.n_fibers[_channel] += 1
self.xifu[_channel].append(float(_x))
self.yifu[_channel].append(float(_y))
self.fib_number[_channel].append(_fib_n)
self.throughput[_channel].append(float(_t))
return f
@property
[docs] def channels(self):
"""
list of channels
"""
return list(self.n_fibers.keys())