# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
"""Utility routines for using the parameter module; as with the
other ciao_contrib.*_wrapper modules it is mainly intended for internal
use and so the API is not guaranteed to be stable.
"""
import os
import ciao_contrib.logger_wrapper as lw
import paramio as pio
logger = lw.initialize_module_logger("param_wrapper")
v5 = logger.verbose5
__all__ = ("open_param_file", )
def show_pfiles():
"""Returns a string listing the directories in the
PFILES environment variable.
"""
try:
pf = os.environ["PFILES"]
except KeyError:
raise IOError("The PFILES environment variable is not set!")
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
__all__ = ["get_radec_from_pos"]
from ciao_contrib.logger_wrapper import initialize_module_logger
logger = initialize_module_logger("parse_pos")
verb0 = logger.verbose0
def _get_radec_from_str(pos):
"""
Get the ra/dec values from the input string.
"""
from coords.format import sex2deg
ps = pos.split(",")
if len(ps) != 2:
ps = pos.split("+")
if len(ps) != 2:
ps = pos.split("-")
if len(ps) != 2:
raise ValueError(
"""
import glob
import json
import os
import subprocess
from urllib.request import urlopen
from urllib.error import HTTPError, URLError
from ciao_contrib import logger_wrapper as lw
__all__ = ('get_installed_versions', 'get_latest_versions',
'read_latest_versions', 'check_conda_versions')
lgr = lw.initialize_module_logger('_tools.versioninfo')
v3 = lgr.verbose3
v4 = lgr.verbose4
def read_vfile(fname):
"Reads the version string from a CIAO version file"
with open(fname, 'r') as fh:
cts = fh.readlines()
# Just take the first line, in case there are any extra new lines
# in the file, as has happened.
return cts[0].strip()
"""
Wrapper around asect solution files.
"""
import numpy as np
import pycrates as pcr
import ciao_contrib.logger_wrapper as lw
import ciao_contrib._tools.fileio as fileio
# __all__ = ("",)
lgr = lw.initialize_module_logger('_tools.aspsol')
v3 = lgr.verbose3
class AspectSolution(object):
"""Represent the aspect solution for an observation. It can consist
of 1 or more aspect solution files. This class deals with sorting
the files in time order.
After creation, the idea is that you use the .name field for
any tool that needs the aspect solution (e.g. asphist.infile or
skyfov.aspect), and nbins for the number of bins to use in
a call to asphist.
If there are multiple files then the .name field will be a
comma-separated list of files. The assumption here is that
As of CIAO 4.6 there should be no need for the PBK (parameter block)
file, but support has been left in.
"""
import os
import pycrates
import stk
from ciao_contrib.logger_wrapper import initialize_module_logger
__all__ = ('find_ancillary_files', 'find_ancillary_files_crate',
'find_ancillary_files_header')
lgr = initialize_module_logger('ancillaryfiles')
v1 = lgr.verbose1
v3 = lgr.verbose3
v4 = lgr.verbose4
__typemap = {
'asol': 'ASOLFILE',
'bpix': 'BPIXFILE',
'dtf': 'DTFFILE',
'flt': 'FLTFILE',
'mask': 'MASKFILE',
'mtl': 'MTLFILE',
'pbk': 'PBKFILE',
# 'thresh': 'THRFILE',
# 'gain': 'GAINFILE',
# 'cti': 'CTIFILE',
__all__ = (
"run",
"punlearn",
"dmcopy",
"update_column_range",
"dmmerge",
"dmimgcalc2", "dmimgcalc", "dmimgcalc_add",
"dmkeypar",
"dmhedit_key", "dmhedit_file",
"get_lookup_table",
"fix_bunit"
# TODO: skyfov
)
lgr = lw.initialize_module_logger('_tools.run')
v2 = lgr.verbose2
v3 = lgr.verbose3
def run(tname, targs):
"""Run the tool (tname) with arguments (targs). Raises an
IOError on failure. Logs the command and arguments at the DEBUG level.
"""
v2(">> Running {}".format(tname))
v2(">> args: {}".format(targs))
args = [tname]
args.extend(targs)
rval = sbp.call(args)
interface. Is it worth it?
"""
import os
import ciao_contrib.ancillaryfiles as ancillary
import ciao_contrib.logger_wrapper as lw
# Can not rely on too many modules in ciao_contrib._tools as do
# not want circular dependencies
import ciao_contrib._tools.fileio as fileio
import ciao_contrib._tools.utils as utils
# __all__ = ("",)
lgr = lw.initialize_module_logger('_tools.obsinfo')
v2 = lgr.verbose2
v3 = lgr.verbose3
def _remove_dmfilter(fname):
"""Return fname stripped of any DM filter,
so '/foo/bar/baz.fits' and '/foo/bar/baz.fits[sky=region(../src.reg)]'
both return '/foo/bar/baz.fits'.
For now only look at DM filter syntax (so anything "[...") but
could also look for CFITSIO syntax ("+<block num>" and "...(copy-name)"),
but only do this if find users actually use this (as unlikely used for
the use cases of this module, although being used more).
"""
"""
Routines that deal with the Chandra field-of-view (FOV)
files created by the skyfov tool (and are also provided as part of
the Chandra standard-data product distribution).
"""
import os
import numpy as np
import pycrates
from ciao_contrib.logger_wrapper import initialize_module_logger
logger = initialize_module_logger("ciao_contrib.region.fov")
v1 = logger.verbose1
v3 = logger.verbose3
v4 = logger.verbose4
v5 = logger.verbose5
__all__ = (
"FOVRegion",
"AxisRange",
)
# not very robust
def _is_int(ival):
"Are we near enough an integer for display purposes?"
import socket
import time
from html.parser import HTMLParser
from urllib.request import urlopen
from urllib.error import URLError
import pycrates
from ciao_contrib import logger_wrapper as lw
__all__ = ("check_caldb_version", "get_caldb_dir", "get_caldb_releases",
"get_caldb_installed", "get_caldb_installed_version",
"get_caldb_installed_date")
lgr = lw.initialize_module_logger('caldb')
v3 = lgr.verbose3
release_notes_url = "https://cxc.cfa.harvard.edu/caldb/downloads/releasenotes.html"
def todate(txt):
"""Convert text to time.
This is intended to convert a time string, as reported by the
CALDB web pages, to a time object.
Parameters
----------
txt : str or None
The time string.
import pycrates
from ciao_contrib.logger_wrapper import initialize_module_logger
from ciao_contrib import smooth as sm
__all__ = (
"make_table_crate", "make_image_crate",
"add_colvals",
"write_columns", "write_arrays",
"scale_image_crate",
"smooth_image_crate",
"SimpleCoordTransform",
"read_ds9_contours",
)
logger = initialize_module_logger("crates_utils")
v3 = logger.verbose3
# time.strftime format to create FITS (like) time format
_fits_time_fmt = "%Y-%m-%dT%H:%M:%S"
def add_colvals(cr, colname, colvals, unit=None, desc=None):
"""Add a new column to the crate.
Create a new column in the crate with the given name and data
values. The unit and desc fields are used to set the column unit
and description if given.
Parameters
import subprocess as sbp
import paramio
import stk
import ciao_contrib.logger_wrapper as lw
import ciao_contrib.runtool as rt
import coords.format
__all__ = ("ObsId", "make_obsid_from_headers", "print_version",
"split_outroot", "to_number", "equal_elements", "getUniqueSynset",
"thresh_is_set", "parse_range", "parse_xygrid", "parse_refpos",
"sky_to_arcsec", "process_tmpdir")
lgr = lw.initialize_module_logger('_tools.utils')
v1 = lgr.verbose1
v3 = lgr.verbose3
v4 = lgr.verbose4
# This is a manually-curated list. It is (as of 2015) not expected
# to grow.
#
_multi_obi_obsids = [
82, 108, 279, 380, 400, 433, 800, 861, 897, 906, 943, 1411, 1431, 1456,
1561, 1578, 2010, 2042, 2077, 2365, 2783, 3057, 3182, 3764, 4175, 60879,
60880, 62249, 62264, 62796
]
def list_multi_obi_obsids():
#
"""
Header routines, currently limited to merging keywords.
The idea is to move this from being text-based to being created with
methods, and having output to text for tools that need it.
"""
import math
import ciao_contrib.logger_wrapper as lw
__all__ = ("HeaderMerge", )
lgr = lw.initialize_module_logger('_tools.merging')
v2 = lgr.verbose2
v3 = lgr.verbose3
v4 = lgr.verbose4
class BaseMergeRule:
"""How should a list of keyword values be combined?
This skips the "warn" part of the header rules.
Parameters
----------
key : str
The name of the keyword.
default : str or None
import sys
import ssl
import time
from io import BytesIO
from subprocess import check_output
import urllib.error
import urllib.request
import http.client
from html.parser import HTMLParser
import ciao_contrib.logger_wrapper as lw
logger = lw.initialize_module_logger("downloadutils")
v0 = logger.verbose0
v1 = logger.verbose1
v2 = logger.verbose1
v3 = logger.verbose3
v4 = logger.verbose4
__all__ = ('retrieve_url', 'find_downloadable_files',
'find_all_downloadable_files', 'ProgressBar', 'download_progress')
def manual_download(url):
"""Try curl then wget to query the URL.
Parameters
For cases when the CADC resolver is not available it falls back to
using the Sesame interface from CDS: http://vizier.u-strasbg.fr/vizier/doc/sesame.htx
"""
from urllib.parse import quote_plus
from urllib.request import urlopen
from urllib.error import HTTPError, URLError
import xml.etree.ElementTree as ET
import ciao_contrib.logger_wrapper as lw
__all__ = ("identify_name", )
logger = lw.initialize_module_logger("cda.resolver")
v4 = logger.verbose4
v5 = logger.verbose5
def strtofloat(val):
"""Convert a string into a float.
The difference to just calling float(val) is that the error
is more user-friendly.
Parameters
----------
val : str
The number to convert
"outfile_clobber_checks",
"rename_file_extension",
"remove_path",
"check_valid_file",
"validate_outdir",
"get_file_from_header",
"get_minmax_times",
# may want to move the following elsewhere
"get_subspace",
"fov_limits",
"get_sky_range",
"find_output_grid",
"get_tangent_point")
lgr = lw.initialize_module_logger('_tools.fileio')
v1 = lgr.verbose1
v2 = lgr.verbose2
v3 = lgr.verbose3
v4 = lgr.verbose4
def get_infile_type(infile):
"""Returns 'Table' or 'Image' depending on what Crates thinks
the type of infile is."""
cr = pycrates.read_file(infile)
return pycrates.get_crate_type(cr)
def get_filter(infile):
"""returns the DM filter used with an input file or stack"""
The API is not guaranteed to remain stable, so use at your own risk.
"""
import os
import sys
import time
from collections import namedtuple
import numpy as np
import cxcdm as dm
from ciao_contrib.logger_wrapper import initialize_module_logger
logger = initialize_module_logger("cxcdm_wrapper")
v1 = logger.verbose3
v3 = logger.verbose3
v5 = logger.verbose5
Record = namedtuple("Record", "name value unit comment")
Column = namedtuple("Column", "name pos type dims unit comment range")
__all__ = ["open_block_from_file", "close_block",
"get_block_info",
"get_block_info_from_file",
"get_info_from_file",
"get_keyword", "get_block_name", "convert_block_number",
"get_obsfiles",
"open_column",
]
import os.path
import ssl
import urllib.parse
import urllib.request
from operator import itemgetter
import ciao_contrib.logger_wrapper as lw
from ciao_contrib import downloadutils
__init__ = ("download_chandra_obsids", )
BASE_URL = 'https://cxc.cfa.harvard.edu/cdaftp/'
LOGGER = lw.initialize_module_logger("cda.data")
V1 = LOGGER.verbose1
V3 = LOGGER.verbose3
__MIRROR_ENVIRON = "CDA_MIRROR_SITE"
def get_mirror_location(useropt):
"""Returns the mirror location, if set, otherwise None. If useropt
is not empty or None then this is returned, otherwise the value of
the CDA_MIRROR_SITE environment variable is returned (if set),
otherwise returns None.
Only minor syntactic checks are made (no attempt is made to
connect to the server).
#
"""
Processing band information (i.e. energy range and representative
energy for instrument maps).
"""
import os
import pycrates
import stk
import ciao_contrib.logger_wrapper as lw
__all__ = ("validate_bands", )
lgr = lw.initialize_module_logger('_tools.bands')
v1 = lgr.verbose1
v3 = lgr.verbose3
def validate_energy_value(enval):
"Error out if enval is outside the nominal energy range of Chandra."
if 0.1 <= enval <= 10.0:
return
raise ValueError(
"Energy of {} keV is outside Chandra's nominal range of 0.1 to 10 keV."
.format(enval))
"""
import numpy as np
from xml.etree import ElementTree
from collections import OrderedDict
import coords.format as coords
import coords.utils as cutils
from ciao_contrib.downloadutils import retrieve_url
import ciao_contrib.logger_wrapper as lw
logger = lw.initialize_module_logger("cda.search")
v3 = logger.verbose3
v4 = logger.verbose4
v5 = logger.verbose5
__all__ = (
"search_chandra_archive",
"get_chandra_obs",
)
def _mkl(label):
return '{http://www.ivoa.net/xml/VOTable/v1.1}' + label
#
# KJG: 2016-09013 no changes needed for P3
"""
Routines related specifically to converting to/from Chandra coordinates
"""
__all__ = ["cel_to_chandra", "sky_to_chandra"]
from pixlib import Pixlib
myPixlib = None
import ciao_contrib.logger_wrapper as lw
logger = lw.initialize_module_logger("coords.chandra")
v0 = logger.verbose0
def _setup_sim(keyword_list):
"""
Get the kewywords related to the SIM location
"""
#
# Get SIM if all keys are present -- should be unless merged then
# all bets are off anyways.
#
if all([x in keyword_list for x in ["SIM_X", "SIM_Y", "SIM_Z"]]):
sim = [
keyword_list["SIM_X"], keyword_list["SIM_Y"], keyword_list["SIM_Z"]
