/usr/lib/python2.7/dist-packages/cpl/recipe.py is in python-cpl 0.7.2-1build2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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import os
import shutil
import tempfile
import threading
import collections
import warnings
import textwrap
try: # pragma: no cover
from astropy.io import fits
except ImportError:
import pyfits as fits
from . import CPL_recipe
from .frames import FrameList, mkabspath, expandframelist
from .result import Result, RecipeCrash
from .param import ParameterList
from .logger import LogServer
class Recipe(object):
'''Pluggable Data Reduction Module (PDRM) from a ESO pipeline.
Recipes are loaded from shared libraries that are provided with the
pipeline library of the instrument. The module does not need to be
linked to the same library version as the one used for the compilation
of python-cpl. Currently, recipes compiled with CPL versions from 4.0
are supported. The list of supported versions is stored as
:attr:`cpl.cpl_versions`.
The libraries are searched in the directories specified by the class
attribute :attr:`Recipe.path` or its subdirectories. The search path is
automatically set to the esorex path when :func:`cpl.esorex.init()`
is called.
'''
path = [ '/usr/lib/x86_64-linux-gnu/cpl/plugins', '/usr/lib/cpl/plugins']
'''Search path for the recipes. It may be set to either a string, or to a
list of strings. All shared libraries in the search path and their
subdirectories are searched for CPL recipes. On default, the path is
set to the current directory.
The search path is automatically set to the esorex path when
:func:`cpl.esorex.init()` is called.
'''
memory_mode = 0
'''CPL memory management mode. The valid values are
0
Use the default system functions for memory handling
1
Exit if a memory-allocation fails, provide checking for memory leaks,
limited reporting of memory allocation and limited protection on
deallocation of invalid pointers.
2
Exit if a memory-allocation fails, provide checking for memory leaks,
extended reporting of memory allocation and protection on deallocation
of invalid pointers.
.. note::
This variable is only effective before the CPL library was
initialized. Even :func:`cpl.Recipe.list()` initializes the library.
Therefore it is highly recommended to set this as the first action after
importing :mod:`cpl`.
'''
def __init__(self, name, filename = None, version = None, threaded = False):
'''Try to load a recipe with the specified name in the directory
specified by the class attribute :attr:`Recipe.path` or its
subdirectories.
:param name: Name of the recipe. Required. Use
:func:`cpl.Recipe.list()` to get a list of available recipes.
:type name: :class:`str`
:param filename: Name of the shared library. Optional. If not set,
:attr:`Recipe.path` is searched for the library file.
:type filename: :class:`str`
:param version: Version number. Optional. If not set, the newest
version is loaded.
:type version: :class:`int` or :class:`str`
:param threaded: Run the recipe in the background, returning
immediately after calling it. Default is :attr:`False`. This may
be also set as an attribute or specified as a parameter when
calling the recipe.
:type threaded: :class:`bool`
'''
os.putenv('CPL_MEMORY_MODE', str(Recipe.memory_mode));
self._recipe = None
self.__name__ = name
'''Recipe name.'''
if not filename:
filename = Recipe.get_recipefilename(name, version)
if not filename:
raise IOError('Recipe %s not found at path %s'
% (repr(name), repr(Recipe.path)))
self.__file__ = filename
'''Shared library file name.'''
self._recipe = CPL_recipe.recipe(filename, name)
if version and version not in self.version:
raise IOError('wrong version %s (requested %s) for %s in %s' %
(str(self.version), str(version), name, filename))
if not self._recipe.cpl_is_supported():
warnings.warn("Unsupported CPL version %s linked to %s" %
(self.cpl_version, filename))
self._param = ParameterList(self)
self._calib = FrameList(self)
self.env = dict()
'''Bla'''
self._tags = None
self.tag = self.tags[0] if self.tags else None
'''Default tag when the recipe is called. This is set automatically
only if the recipe provided the information about input
tags. Otherwise this tag has to be set manually.
'''
self.output_dir = None
self.temp_dir = '.'
'''Base directory for temporary directories where the recipe is
executed. The working dir is created as a subdir with a random file
name. If set to :obj:`None`, the system temp dir is used. Defaults to
:literal:`'.'`.
'''
self.memory_dump = 0
self.threaded = threaded
self.mtrace = False
self.__doc__ = self._doc()
@property
def __author__(self):
'''Author name'''
return self._recipe.author()[0]
@property
def __email__(self):
'''Author email'''
return self._recipe.author()[1]
@property
def description(self):
'''Pair (synopsis, description) of two strings.'''
return self._recipe.description()
@property
def version(self):
'''Pair (versionnumber, versionstring) of an integer and a string.
The integer will be increased on development progress.'''
return self._recipe.version()
@property
def __version__(self):
return self._recipe.version()[1]
@property
def __copyright__(self):
'''Copyright string of the recipe'''
return self._recipe.copyright()
@property
def cpl_version(self):
'''Version of the CPL library that is linked to the recipe,
as a string'''
return self._recipe.cpl_version()
@property
def cpl_description(self):
'''Version numbers of CPL and its libraries that were linked to
the recipe, as a string.'''
return self._recipe.cpl_description()
@property
def tags(self):
'''Possible tags for the raw input frames, or ':obj:`None` if this
information is not provided by the recipe.'''
frameconfig = self._recipe.frameConfig()
return [ c[0][0] for c in frameconfig ] if frameconfig else self._tags
@tags.setter
def tags(self, t):
if self._recipe.frameConfig():
raise AttributeError('Tags are immutable')
else:
self._tags = t
@property
def tag(self):
'''Default raw input frame tag. After creation, it is set to the first
tag from the "tags" property and may be changed to any of these
tags. If the recipe does not provide the tag information, it must be
set manually, or the tag name has to be provided when calling the
recipe.'''
return self._tag
@tag.setter
def tag(self, t):
if self.tags is None or t in self.tags:
self._tag = t
else:
raise KeyError("Tag %s not in %s" % (repr(t), str(self.tags)))
@property
def calib(self):
'''This attribute contains the calibration frames
for the recipe. It is iterable and then returns all calibration frames:
>>> for f in muse_scibasic.calib:
... print f.tag, f.min, f.max, f.frames
TRACE_TABLE 1 1 None
WAVECAL_TABLE 1 1 None
MASTER_BIAS 1 1 master_bias_0.fits
MASTER_DARK None 1 None
GEOMETRY_TABLE 1 1 None
BADPIX_TABLE None None ['badpix_1.fits', 'badpix_2.fits']
MASTER_FLAT None 1 None
.. note::
Only MUSE recipes are able to provide the full list of
calibration frames and the minimal/maximal number of calibration
frames. For other recipes, only frames that were set by the users are
returned here. Their minimum and maximum value will be set to
:obj:`None`.
In order to assing a FITS file to a tag, the file name or the
:class:`astropy.io.fits.HDUList` is assigned to the calibration
attribute:
>>> muse_scibasic.calib.MASTER_BIAS = 'MASTER_BIAS_0.fits'
Using :class:`astropy.io.fits.HDUList` is useful when it needs to be
patched before fed into the recipe.
>>> master_bias = astropy.io.fits.open('MASTER_BIAS_0.fits')
>>> master_bias[0].header['HIERARCH ESO DET CHIP1 OUT1 GAIN'] = 2.5
>>> muse_scibasic.calib.MASTER_BIAS = master_bias
Note that :class:`astropy.io.fits.HDUList` objects are stored in
temporary files before the recipe is called which may produce some
overhead. Also, the CPL then assigns the random temporary file names
to the FITS keywords ``HIERARCH ESO PRO RECm RAWn NAME`` which should
be corrected afterwards if needed.
To assign more than one frame, put them into a list:
>>> muse_scibasic.calib.BADPIX_TABLE = [ 'badpix1.fits', 'badpix2.fits' ]
All calibration frames can be set in one step by assigning a
:class:`dict` to the parameters. In this case, frame that are not in
the map are set are removed from the list, and unknown frame tags are
silently ignored. The key of the map is the tag name; the values are
either a string, or a list of strings, containing the file name(s) or
the :class:`astropy.io.fits.HDUList` objects.
>>> muse_scibasic.calib = { 'MASTER_BIAS':'master_bias_0.fits',
... 'BADPIX_TABLE':[ 'badpix_1.fits', 'badpix_2.fits' ] }
In a recipe call, the calibration frame lists may be overwritten by
specifying them in a :class:`dict`:
>>> res = muse_scibasic( ..., calib = {'MASTER_BIAS':'master_bias_1.fits'})
'''
return self._calib
@calib.setter
def calib(self, source = None):
if isinstance(source, str) or hasattr(source, 'read'):
from .esorex import load_sof
source = load_sof(source)
self._calib = FrameList(self, source)
@calib.deleter
def calib(self):
self._calib = FrameList(self, None)
@property
def param(self):
'''This attribute contains all recipe parameters.
It is iteratable and then returns all individual parameters:
>>> for p in muse_scibasic.param:
... print p.name, p.value, p.default
...
nifu None 99
cr None dcr
xbox None 15
ybox None 40
passes None 2
thres None 4.5
sample None False
dlambda None 1.2
On interactive sessions, all parameter settings can be easily printed by
printing the :attr:`param` attribute of the recipe:
>>> print muse_scibasic.param
[Parameter('nifu', default=99), Parameter('cr', default=dcr),
Parameter('xbox', default=15), Parameter('ybox', default=40),
Parameter('passes', default=2), Parameter('thres', default=4.5),
Parameter('sample', default=False), Parameter('dlambda', default=1.2)]
To set the value of a recipe parameter, the value can be assigned to
the according attribute:
>>> muse_scibasic.param.nifu = 1
The new value is checked against parameter type, and possible value
limitations provided by the recipe. Hyphens in parameter names are
converted to underscores. In a recipe call, the same parameter can be
specified as :class:`dict`:
>>> res = muse_scibasic( ..., param = {'nifu':1})
To reset a value to its default, it is either deleted, or set to
:obj:`None`. The following two lines:
>>> muse_scibasic.param.nifu = None
>>> del muse_scibasic.param.nifu
will both reset the parameter to its default value.
All parameters can be set in one step by assigning a :class:`dict` to
the parameters. In this case, all values that are not in the map are
reset to default, and unknown parameter names are ignored. The keys of
the map may contain contain the name or the fullname with context:
>>> muse_scibasic.param = { 'nifu':1, 'xbox':11, 'resample':True }
'''
return self._param
@param.setter
def param(self, source = None):
if isinstance(source, str) or hasattr(source, 'read'):
from .esorex import load_rc
source = load_rc(source)
self._param = ParameterList(self, source)
@param.deleter
def param(self):
self._param = ParameterList(self, None)
@property
def output(self):
'''Return a dictionary of output frame tags.
Keys are the tag names, values are the corresponding list of output
tags. If the recipe does not provide this information, an exception is
raised.
'''
return dict((c[0][0], c[2]) for c in self._recipe.frameConfig())
def __call__(self, *data, **ndata):
'''Call the recipes execution with a certain input frame.
:param raw: Data input frames.
:type raw: :class:`astropy.io.fits.HDUlist` or :class:`str` or a
:class:`list` of them, or :class:`dict`
:param tag: Overwrite the :attr:`tag` attribute (optional).
:type tag: :class:`str`
:param threaded: overwrite the :attr:`threaded` attribute (optional).
:type threaded: :class:`bool`
:param loglevel: set the log level for python :mod:`logging` (optional).
:type loglevel: :class:`int`
:param logname: set the log name for the python
:class:`logging.Logger` (optional, default is 'cpl.' + recipename).
:type logname: :class:`str`
:param output_dir: Set or overwrite the :attr:`output_dir` attribute.
(optional)
:type output_dir: :class:`str`
:param param: overwrite the CPL parameters of the recipe specified
as keys with their dictionary values (optional).
:type param: :class:`dict`
:param calib: Overwrite the calibration frame lists for the tags
specified as keys with their dictionary values (optional).
:type calib: :class:`dict`
:param env: overwrite environment variables for the recipe call
(optional).
:type env: :class:`dict`
:return: The object with the return frames as
:class:`astropy.io.fits.HDUList` objects
:rtype: :class:`cpl.Result`
:raise: :exc:`exceptions.ValueError` If the invocation parameters
are incorrect.
:raise: :exc:`exceptions.IOError` If the temporary directory could
not be built, the recipe could not start or the files could not
be read/written.
:raise: :exc:`cpl.CplError` If the recipe returns an error.
:raise: :exc:`cpl.RecipeCrash` If the CPL recipe crashes with a
SIGSEV or a SIGBUS
.. note::
If the recipe is executed in the background
(``threaded = True``) and an exception occurs, this exception is
raised whenever result fields are accessed.
'''
threaded = ndata.get('threaded', self.threaded)
mtrace = ndata.get('mtrace', self.mtrace)
loglevel = ndata.get('loglevel')
logname = ndata.get('logname', 'cpl.%s' % self.__name__)
output_dir = ndata.get('output_dir', self.output_dir)
output_format = str if output_dir else fits.HDUList
if output_dir is None:
output_dir = tempfile.mkdtemp(dir = self.temp_dir,
prefix = self.__name__ + "-")
parlist = self.param._aslist(ndata.get('param'))
raw_frames = self._get_raw_frames(*data, **ndata)
if len(raw_frames) < 1:
raise ValueError('No raw frames specified.')
input_len = -1 if isinstance(raw_frames[0][1], fits.HDUList) else \
len(raw_frames[0][1]) if isinstance(raw_frames[0][1], list) else -1
calib_frames = self.calib._aslist(ndata.get('calib'))
framelist = expandframelist(raw_frames + calib_frames)
runenv = dict(self.env)
runenv.update(ndata.get('env', dict()))
logger = None
delete = output_format == fits.HDUList
try:
if (not os.access(output_dir, os.F_OK)):
os.makedirs(output_dir)
mkabspath(framelist, output_dir)
logger = LogServer(logname, loglevel)
except:
try:
self._cleanup(output_dir, logger, delete)
except:
pass
raise
if not threaded:
return self._exec(output_dir, parlist, framelist, runenv,
input_len, logger, output_format, delete, mtrace)
else:
return Threaded(
self._exec, output_dir, parlist, framelist, runenv,
input_len, logger, output_format, delete, mtrace)
def _exec(self, output_dir, parlist, framelist, runenv,
input_len, logger, output_format, delete, mtrace):
try:
return Result(output_dir,
self._recipe.run(output_dir, parlist, framelist,
list(runenv.items()),
logger.logfile, logger.level,
self.memory_dump, mtrace),
input_len, logger, output_format)
finally:
self._cleanup(output_dir, logger, delete)
def _get_raw_frames(self, *data, **ndata):
'''Return the input frames.
Returns a :class:`list` with (tag, the input frame(s)) pairs. Note
that more than one input tag is not allowed here.
'''
data = list(data)
if 'raw' in ndata:
data.append(ndata['raw'])
tag = ndata.get('tag', self.tag)
m = { }
for f in data:
if isinstance(f, dict):
m.update(f)
elif tag is None:
raise ValueError('No raw input tag')
elif tag not in m:
m[tag] = f
elif isinstance(m[tag], list) \
and not isinstance(m[tag], fits.HDUList):
m[tag].append(f)
else:
m[tag] = [ m[tag], f ]
return list(m.items())
def _cleanup(self, output_dir, logger, delete):
try:
bt = os.path.join(output_dir, 'recipe.backtrace-unprocessed')
if os.path.exists(bt):
with open(bt) as bt_file:
os.rename(bt, os.path.join(output_dir, 'recipe.backtrace'))
ex = RecipeCrash(bt_file)
ex.log(logger.logger)
raise ex
finally:
if delete:
shutil.rmtree(output_dir)
def _doc(self):
s = '%s\n\n%s\n\n' % (textwrap.fill(self.description[0]),
textwrap.fill(self.description[1]))
if len(self.param) > 0:
r = 'Parameters:\n%s\n' % self._param.__doc__
else:
r = 'No parameters\n'
if self._recipe.frameConfig() is not None:
c = textwrap.fill(repr([f.tag for f in self.calib]),
initial_indent = 'Calibration frames: ',
subsequent_indent = ' ' * 21) + '\n\n'
else:
c = ''
if self.tags is not None:
t = 'Raw and product frames:\n'
maxlen = max(len(f) for f in self.tags)
for f in self.tags:
t += textwrap.fill(repr(self.output[f]),
initial_indent = ' %s --> ' % f.rjust(maxlen),
subsequent_indent = ' ' * (maxlen + 7)) + '\n'
else:
t = ''
return s + r + c + t + '\n\n'
def __repr__(self):
return 'Recipe(%s, version = %s)' % (repr(self.__name__),
repr(self.version[0]))
@staticmethod
def list():
'''Return a list of recipes.
Searches for all recipes in in the directory specified by the class
attribute :attr:`Recipe.path` or its subdirectories.
'''
os.putenv('CPL_MEMORY_MODE', str(Recipe.memory_mode));
plugins = collections.defaultdict(list)
for f in Recipe.get_libs():
plugin_f = CPL_recipe.list(f)
if plugin_f:
for p in plugin_f:
plugins[p[0]].append(p[2])
return list(plugins.items())
@staticmethod
def get_recipefilename(name, version = None):
os.putenv('CPL_MEMORY_MODE', str(Recipe.memory_mode));
filename = None
rversion = -1
for f in Recipe.get_libs():
plugin_f = CPL_recipe.list(f)
if plugin_f:
for p in plugin_f:
if p[0] != name:
continue
if version in p[1:3]:
return f
if rversion < p[1]:
rversion = p[1]
filename = f
return filename
@staticmethod
def get_libs():
libs = [ ]
path = Recipe.path.split(':') if isinstance(Recipe.path, str) else Recipe.path
for p in path:
for root, d, files in os.walk(p):
libs += [ os.path.join(root, f)
for f in files if f.endswith('.so') ]
return libs
@staticmethod
def set_maxthreads(n):
'''Set the maximal number of threads to be executed in parallel.
.. note::
This affects only threads that are started afterwards with
the ``threaded = True`` flag.
.. seealso:: :ref:`parallel`
'''
Threaded.set_maxthreads(n)
class Threaded(threading.Thread):
'''Simple threading interface.
Creating this object will start the execution of func(*args, **nargs).
It returns an object that has the same attribute as the function return
value, if the function execution was completed.
Accessing any of the attributes will cause a wait until the function
execution is ready. Note that the attribute delegation will work only for
attributes (not for methods), and it will not work for attributes defined
by the threading.Thread interface.
If the function returns an exception, this exception is thrown by any
attempt to access an attribute.
'''
pool_sema = threading.BoundedSemaphore(65536)
def __init__(self, func, *args, **nargs):
threading.Thread.__init__(self)
self._func = func
self._args = args
self._nargs = nargs
self._res = None
self._exception = None
self.start()
def run(self):
with Threaded.pool_sema:
try:
self._res = self._func(*self._args, **self._nargs)
except Exception as exception:
self._exception = exception
@property
def _result(self):
self.join()
if self._exception is None:
return self._res
else:
raise self._exception
def __getitem__(self, key):
return self._result[key]
def __contains__(self, key):
return key in self._result.tags
def __len__(self):
return len(self._result.tags)
def __iter__(self):
return self._result.__iter__()
def __getattr__(self, name):
return self._result.__dict__[name]
@staticmethod
def set_maxthreads(n):
with Threaded.pool_sema:
Threaded.pool_sema = threading.BoundedSemaphore(n)
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