# getargspec and formatargspec were removed in Python 3.6
'issubclass_', 'issubsctype', 'issubdtype', 'deprecate', 'deprecate_with_doc', 'get_include', 'info', 'source', 'who', 'lookfor', 'byte_bounds', 'safe_eval' ]
""" Return the directory that contains the NumPy \\*.h header files.
Extension modules that need to compile against NumPy should use this function to locate the appropriate include directory.
Notes ----- When using ``distutils``, for example in ``setup.py``. ::
import numpy as np ... Extension('extension_name', ... include_dirs=[np.get_include()]) ...
""" import numpy if numpy.show_config is None: # running from numpy source directory d = os.path.join(os.path.dirname(numpy.__file__), 'core', 'include') else: # using installed numpy core headers import numpy.core as core d = os.path.join(os.path.dirname(core.__file__), 'include') return d
""" Decorator class to deprecate old functions.
Refer to `deprecate` for details.
See Also -------- deprecate
"""
""" Decorator call. Refer to ``decorate``.
"""
except AttributeError: old_name = func.__name__ else: (old_name, new_name)
"""`arrayrange` is deprecated, use `arange` instead!""" warnings.warn(depdoc, DeprecationWarning, stacklevel=2) return func(*args, **kwds)
else: else:
""" Issues a DeprecationWarning, adds warning to `old_name`'s docstring, rebinds ``old_name.__name__`` and returns the new function object.
This function may also be used as a decorator.
Parameters ---------- func : function The function to be deprecated. old_name : str, optional The name of the function to be deprecated. Default is None, in which case the name of `func` is used. new_name : str, optional The new name for the function. Default is None, in which case the deprecation message is that `old_name` is deprecated. If given, the deprecation message is that `old_name` is deprecated and `new_name` should be used instead. message : str, optional Additional explanation of the deprecation. Displayed in the docstring after the warning.
Returns ------- old_func : function The deprecated function.
Examples -------- Note that ``olduint`` returns a value after printing Deprecation Warning:
>>> olduint = np.deprecate(np.uint) >>> olduint(6) /usr/lib/python2.5/site-packages/numpy/lib/utils.py:114: DeprecationWarning: uint32 is deprecated warnings.warn(str1, DeprecationWarning, stacklevel=2) 6
""" # Deprecate may be run as a function or as a decorator # If run as a function, we initialise the decorator class # and execute its __call__ method.
else:
#-------------------------------------------- # Determine if two arrays can share memory #--------------------------------------------
""" Returns pointers to the end-points of an array.
Parameters ---------- a : ndarray Input array. It must conform to the Python-side of the array interface.
Returns ------- (low, high) : tuple of 2 integers The first integer is the first byte of the array, the second integer is just past the last byte of the array. If `a` is not contiguous it will not use every byte between the (`low`, `high`) values.
Examples -------- >>> I = np.eye(2, dtype='f'); I.dtype dtype('float32') >>> low, high = np.byte_bounds(I) >>> high - low == I.size*I.itemsize True >>> I = np.eye(2, dtype='G'); I.dtype dtype('complex192') >>> low, high = np.byte_bounds(I) >>> high - low == I.size*I.itemsize True
""" ai = a.__array_interface__ a_data = ai['data'][0] astrides = ai['strides'] ashape = ai['shape'] bytes_a = asarray(a).dtype.itemsize
a_low = a_high = a_data if astrides is None: # contiguous case a_high += a.size * bytes_a else: for shape, stride in zip(ashape, astrides): if stride < 0: a_low += (shape-1)*stride else: a_high += (shape-1)*stride a_high += bytes_a return a_low, a_high
#----------------------------------------------------------------------------- # Function for output and information on the variables used. #-----------------------------------------------------------------------------
""" Print the NumPy arrays in the given dictionary.
If there is no dictionary passed in or `vardict` is None then returns NumPy arrays in the globals() dictionary (all NumPy arrays in the namespace).
Parameters ---------- vardict : dict, optional A dictionary possibly containing ndarrays. Default is globals().
Returns ------- out : None Returns 'None'.
Notes ----- Prints out the name, shape, bytes and type of all of the ndarrays present in `vardict`.
Examples -------- >>> a = np.arange(10) >>> b = np.ones(20) >>> np.who() Name Shape Bytes Type =========================================================== a 10 40 int32 b 20 160 float64 Upper bound on total bytes = 200
>>> d = {'x': np.arange(2.0), 'y': np.arange(3.0), 'txt': 'Some str', ... 'idx':5} >>> np.who(d) Name Shape Bytes Type =========================================================== y 3 24 float64 x 2 16 float64 Upper bound on total bytes = 40
""" if vardict is None: frame = sys._getframe().f_back vardict = frame.f_globals sta = [] cache = {} for name in vardict.keys(): if isinstance(vardict[name], ndarray): var = vardict[name] idv = id(var) if idv in cache.keys(): namestr = name + " (%s)" % cache[idv] original = 0 else: cache[idv] = name namestr = name original = 1 shapestr = " x ".join(map(str, var.shape)) bytestr = str(var.nbytes) sta.append([namestr, shapestr, bytestr, var.dtype.name, original])
maxname = 0 maxshape = 0 maxbyte = 0 totalbytes = 0 for k in range(len(sta)): val = sta[k] if maxname < len(val[0]): maxname = len(val[0]) if maxshape < len(val[1]): maxshape = len(val[1]) if maxbyte < len(val[2]): maxbyte = len(val[2]) if val[4]: totalbytes += int(val[2])
if len(sta) > 0: sp1 = max(10, maxname) sp2 = max(10, maxshape) sp3 = max(10, maxbyte) prval = "Name %s Shape %s Bytes %s Type" % (sp1*' ', sp2*' ', sp3*' ') print(prval + "\n" + "="*(len(prval)+5) + "\n")
for k in range(len(sta)): val = sta[k] print("%s %s %s %s %s %s %s" % (val[0], ' '*(sp1-len(val[0])+4), val[1], ' '*(sp2-len(val[1])+5), val[2], ' '*(sp3-len(val[2])+5), val[3])) print("\nUpper bound on total bytes = %d" % totalbytes) return
#-----------------------------------------------------------------------------
# NOTE: pydoc defines a help function which works similarly to this # except it uses a pager to take over the screen.
# combine name and arguments and split to multiple lines of width # characters. End lines on a comma and begin argument list indented with # the rest of the arguments. firstwidth = len(name) k = firstwidth newstr = name sepstr = ", " arglist = arguments.split(sepstr) for argument in arglist: if k == firstwidth: addstr = "" else: addstr = sepstr k = k + len(argument) + len(addstr) if k > width: k = firstwidth + 1 + len(argument) newstr = newstr + ",\n" + " "*(firstwidth+2) + argument else: newstr = newstr + addstr + argument return newstr
# Traverse all module directories underneath globals # to see if something is defined module = __import__(module, globals(), locals(), []) thedict = {module.__name__:module.__dict__} dictlist = [module.__name__] totraverse = [module.__dict__] while True: if len(totraverse) == 0: break thisdict = totraverse.pop(0) for x in thisdict.keys(): if isinstance(thisdict[x], types.ModuleType): modname = thisdict[x].__name__ if modname not in dictlist: moddict = thisdict[x].__dict__ dictlist.append(modname) totraverse.append(moddict) thedict[modname] = moddict return thedict, dictlist
"""Provide information about ndarray obj.
Parameters ---------- obj : ndarray Must be ndarray, not checked. output Where printed output goes.
Notes ----- Copied over from the numarray module prior to its removal. Adapted somewhat as only numpy is an option now.
Called by info.
""" extra = "" tic = "" bp = lambda x: x cls = getattr(obj, '__class__', type(obj)) nm = getattr(cls, '__name__', cls) strides = obj.strides endian = obj.dtype.byteorder
print("class: ", nm, file=output) print("shape: ", obj.shape, file=output) print("strides: ", strides, file=output) print("itemsize: ", obj.itemsize, file=output) print("aligned: ", bp(obj.flags.aligned), file=output) print("contiguous: ", bp(obj.flags.contiguous), file=output) print("fortran: ", obj.flags.fortran, file=output) print( "data pointer: %s%s" % (hex(obj.ctypes._as_parameter_.value), extra), file=output ) print("byteorder: ", end=' ', file=output) if endian in ['|', '=']: print("%s%s%s" % (tic, sys.byteorder, tic), file=output) byteswap = False elif endian == '>': print("%sbig%s" % (tic, tic), file=output) byteswap = sys.byteorder != "big" else: print("%slittle%s" % (tic, tic), file=output) byteswap = sys.byteorder != "little" print("byteswap: ", bp(byteswap), file=output) print("type: %s" % obj.dtype, file=output)
""" Get help information for a function, class, or module.
Parameters ---------- object : object or str, optional Input object or name to get information about. If `object` is a numpy object, its docstring is given. If it is a string, available modules are searched for matching objects. If None, information about `info` itself is returned. maxwidth : int, optional Printing width. output : file like object, optional File like object that the output is written to, default is ``stdout``. The object has to be opened in 'w' or 'a' mode. toplevel : str, optional Start search at this level.
See Also -------- source, lookfor
Notes ----- When used interactively with an object, ``np.info(obj)`` is equivalent to ``help(obj)`` on the Python prompt or ``obj?`` on the IPython prompt.
Examples -------- >>> np.info(np.polyval) # doctest: +SKIP polyval(p, x) Evaluate the polynomial p at x. ...
When using a string for `object` it is possible to get multiple results.
>>> np.info('fft') # doctest: +SKIP *** Found in numpy *** Core FFT routines ... *** Found in numpy.fft *** fft(a, n=None, axis=-1) ... *** Repeat reference found in numpy.fft.fftpack *** *** Total of 3 references found. ***
""" global _namedict, _dictlist # Local import to speed up numpy's import time. import pydoc import inspect
if (hasattr(object, '_ppimport_importer') or hasattr(object, '_ppimport_module')): object = object._ppimport_module elif hasattr(object, '_ppimport_attr'): object = object._ppimport_attr
if object is None: info(info) elif isinstance(object, ndarray): _info(object, output=output) elif isinstance(object, str): if _namedict is None: _namedict, _dictlist = _makenamedict(toplevel) numfound = 0 objlist = [] for namestr in _dictlist: try: obj = _namedict[namestr][object] if id(obj) in objlist: print("\n " "*** Repeat reference found in %s *** " % namestr, file=output ) else: objlist.append(id(obj)) print(" *** Found in %s ***" % namestr, file=output) info(obj) print("-"*maxwidth, file=output) numfound += 1 except KeyError: pass if numfound == 0: print("Help for %s not found." % object, file=output) else: print("\n " "*** Total of %d references found. ***" % numfound, file=output )
elif inspect.isfunction(object): name = object.__name__ arguments = formatargspec(*getargspec(object))
if len(name+arguments) > maxwidth: argstr = _split_line(name, arguments, maxwidth) else: argstr = name + arguments
print(" " + argstr + "\n", file=output) print(inspect.getdoc(object), file=output)
elif inspect.isclass(object): name = object.__name__ arguments = "()" try: if hasattr(object, '__init__'): arguments = formatargspec( *getargspec(object.__init__.__func__) ) arglist = arguments.split(', ') if len(arglist) > 1: arglist[1] = "("+arglist[1] arguments = ", ".join(arglist[1:]) except Exception: pass
if len(name+arguments) > maxwidth: argstr = _split_line(name, arguments, maxwidth) else: argstr = name + arguments
print(" " + argstr + "\n", file=output) doc1 = inspect.getdoc(object) if doc1 is None: if hasattr(object, '__init__'): print(inspect.getdoc(object.__init__), file=output) else: print(inspect.getdoc(object), file=output)
methods = pydoc.allmethods(object) if methods != []: print("\n\nMethods:\n", file=output) for meth in methods: if meth[0] == '_': continue thisobj = getattr(object, meth, None) if thisobj is not None: methstr, other = pydoc.splitdoc( inspect.getdoc(thisobj) or "None" ) print(" %s -- %s" % (meth, methstr), file=output)
elif (sys.version_info[0] < 3 and isinstance(object, types.InstanceType)): # check for __call__ method # types.InstanceType is the type of the instances of oldstyle classes print("Instance of class: ", object.__class__.__name__, file=output) print(file=output) if hasattr(object, '__call__'): arguments = formatargspec( *getargspec(object.__call__.__func__) ) arglist = arguments.split(', ') if len(arglist) > 1: arglist[1] = "("+arglist[1] arguments = ", ".join(arglist[1:]) else: arguments = "()"
if hasattr(object, 'name'): name = "%s" % object.name else: name = "<name>" if len(name+arguments) > maxwidth: argstr = _split_line(name, arguments, maxwidth) else: argstr = name + arguments
print(" " + argstr + "\n", file=output) doc = inspect.getdoc(object.__call__) if doc is not None: print(inspect.getdoc(object.__call__), file=output) print(inspect.getdoc(object), file=output)
else: print(inspect.getdoc(object), file=output)
elif inspect.ismethod(object): name = object.__name__ arguments = formatargspec( *getargspec(object.__func__) ) arglist = arguments.split(', ') if len(arglist) > 1: arglist[1] = "("+arglist[1] arguments = ", ".join(arglist[1:]) else: arguments = "()"
if len(name+arguments) > maxwidth: argstr = _split_line(name, arguments, maxwidth) else: argstr = name + arguments
print(" " + argstr + "\n", file=output) print(inspect.getdoc(object), file=output)
elif hasattr(object, '__doc__'): print(inspect.getdoc(object), file=output)
""" Print or write to a file the source code for a NumPy object.
The source code is only returned for objects written in Python. Many functions and classes are defined in C and will therefore not return useful information.
Parameters ---------- object : numpy object Input object. This can be any object (function, class, module, ...). output : file object, optional If `output` not supplied then source code is printed to screen (sys.stdout). File object must be created with either write 'w' or append 'a' modes.
See Also -------- lookfor, info
Examples -------- >>> np.source(np.interp) #doctest: +SKIP In file: /usr/lib/python2.6/dist-packages/numpy/lib/function_base.py def interp(x, xp, fp, left=None, right=None): \"\"\".... (full docstring printed)\"\"\" if isinstance(x, (float, int, number)): return compiled_interp([x], xp, fp, left, right).item() else: return compiled_interp(x, xp, fp, left, right)
The source code is only returned for objects written in Python.
>>> np.source(np.array) #doctest: +SKIP Not available for this object.
""" # Local import to speed up numpy's import time. import inspect try: print("In file: %s\n" % inspect.getsourcefile(object), file=output) print(inspect.getsource(object), file=output) except Exception: print("Not available for this object.", file=output)
# Cache for lookfor: {id(module): {name: (docstring, kind, index), ...}...} # where kind: "func", "class", "module", "object" # and index: index in breadth-first namespace traversal
# regexp whose match indicates that the string may contain a function # signature
output=None): """ Do a keyword search on docstrings.
A list of objects that matched the search is displayed, sorted by relevance. All given keywords need to be found in the docstring for it to be returned as a result, but the order does not matter.
Parameters ---------- what : str String containing words to look for. module : str or list, optional Name of module(s) whose docstrings to go through. import_modules : bool, optional Whether to import sub-modules in packages. Default is True. regenerate : bool, optional Whether to re-generate the docstring cache. Default is False. output : file-like, optional File-like object to write the output to. If omitted, use a pager.
See Also -------- source, info
Notes ----- Relevance is determined only roughly, by checking if the keywords occur in the function name, at the start of a docstring, etc.
Examples -------- >>> np.lookfor('binary representation') Search results for 'binary representation' ------------------------------------------ numpy.binary_repr Return the binary representation of the input number as a string. numpy.core.setup_common.long_double_representation Given a binary dump as given by GNU od -b, look for long double numpy.base_repr Return a string representation of a number in the given base system. ...
""" import pydoc
# Cache cache = _lookfor_generate_cache(module, import_modules, regenerate)
# Search # XXX: maybe using a real stemming search engine would be better? found = [] whats = str(what).lower().split() if not whats: return
for name, (docstring, kind, index) in cache.items(): if kind in ('module', 'object'): # don't show modules or objects continue ok = True doc = docstring.lower() for w in whats: if w not in doc: ok = False break if ok: found.append(name)
# Relevance sort # XXX: this is full Harrison-Stetson heuristics now, # XXX: it probably could be improved
kind_relevance = {'func': 1000, 'class': 1000, 'module': -1000, 'object': -1000}
def relevance(name, docstr, kind, index): r = 0 # do the keywords occur within the start of the docstring? first_doc = "\n".join(docstr.lower().strip().split("\n")[:3]) r += sum([200 for w in whats if w in first_doc]) # do the keywords occur in the function name? r += sum([30 for w in whats if w in name]) # is the full name long? r += -len(name) * 5 # is the object of bad type? r += kind_relevance.get(kind, -1000) # is the object deep in namespace hierarchy? r += -name.count('.') * 10 r += max(-index / 100, -100) return r
def relevance_value(a): return relevance(a, *cache[a]) found.sort(key=relevance_value)
# Pretty-print s = "Search results for '%s'" % (' '.join(whats)) help_text = [s, "-"*len(s)] for name in found[::-1]: doc, kind, ix = cache[name]
doclines = [line.strip() for line in doc.strip().split("\n") if line.strip()]
# find a suitable short description try: first_doc = doclines[0].strip() if _function_signature_re.search(first_doc): first_doc = doclines[1].strip() except IndexError: first_doc = "" help_text.append("%s\n %s" % (name, first_doc))
if not found: help_text.append("Nothing found.")
# Output if output is not None: output.write("\n".join(help_text)) elif len(help_text) > 10: pager = pydoc.getpager() pager("\n".join(help_text)) else: print("\n".join(help_text))
""" Generate docstring cache for given module.
Parameters ---------- module : str, None, module Module for which to generate docstring cache import_modules : bool Whether to import sub-modules in packages. regenerate : bool Re-generate the docstring cache
Returns ------- cache : dict {obj_full_name: (docstring, kind, index), ...} Docstring cache for the module, either cached one (regenerate=False) or newly generated.
""" global _lookfor_caches # Local import to speed up numpy's import time. import inspect
if sys.version_info[0] >= 3: # In Python3 stderr, stdout are text files. from io import StringIO else: from StringIO import StringIO
if module is None: module = "numpy"
if isinstance(module, str): try: __import__(module) except ImportError: return {} module = sys.modules[module] elif isinstance(module, list) or isinstance(module, tuple): cache = {} for mod in module: cache.update(_lookfor_generate_cache(mod, import_modules, regenerate)) return cache
if id(module) in _lookfor_caches and not regenerate: return _lookfor_caches[id(module)]
# walk items and collect docstrings cache = {} _lookfor_caches[id(module)] = cache seen = {} index = 0 stack = [(module.__name__, module)] while stack: name, item = stack.pop(0) if id(item) in seen: continue seen[id(item)] = True
index += 1 kind = "object"
if inspect.ismodule(item): kind = "module" try: _all = item.__all__ except AttributeError: _all = None
# import sub-packages if import_modules and hasattr(item, '__path__'): for pth in item.__path__: for mod_path in os.listdir(pth): this_py = os.path.join(pth, mod_path) init_py = os.path.join(pth, mod_path, '__init__.py') if (os.path.isfile(this_py) and mod_path.endswith('.py')): to_import = mod_path[:-3] elif os.path.isfile(init_py): to_import = mod_path else: continue if to_import == '__init__': continue
try: old_stdout = sys.stdout old_stderr = sys.stderr try: sys.stdout = StringIO() sys.stderr = StringIO() __import__("%s.%s" % (name, to_import)) finally: sys.stdout = old_stdout sys.stderr = old_stderr # Catch SystemExit, too except BaseException: continue
for n, v in _getmembers(item): try: item_name = getattr(v, '__name__', "%s.%s" % (name, n)) mod_name = getattr(v, '__module__', None) except NameError: # ref. SWIG's global cvars # NameError: Unknown C global variable item_name = "%s.%s" % (name, n) mod_name = None if '.' not in item_name and mod_name: item_name = "%s.%s" % (mod_name, item_name)
if not item_name.startswith(name + '.'): # don't crawl "foreign" objects if isinstance(v, ufunc): # ... unless they are ufuncs pass else: continue elif not (inspect.ismodule(v) or _all is None or n in _all): continue stack.append(("%s.%s" % (name, n), v)) elif inspect.isclass(item): kind = "class" for n, v in _getmembers(item): stack.append(("%s.%s" % (name, n), v)) elif hasattr(item, "__call__"): kind = "func"
try: doc = inspect.getdoc(item) except NameError: # ref SWIG's NameError: Unknown C global variable doc = None if doc is not None: cache[name] = (doc, kind, index)
return cache
import inspect try: members = inspect.getmembers(item) except Exception: members = [(x, getattr(item, x)) for x in dir(item) if hasattr(item, x)] return members
#-----------------------------------------------------------------------------
# The following SafeEval class and company are adapted from Michael Spencer's # ASPN Python Cookbook recipe: https://code.activestate.com/recipes/364469/ # # Accordingly it is mostly Copyright 2006 by Michael Spencer. # The recipe, like most of the other ASPN Python Cookbook recipes was made # available under the Python license. # https://en.wikipedia.org/wiki/Python_License
# It has been modified to: # * handle unary -/+ # * support True/False/None # * raise SyntaxError instead of a custom exception.
""" Object to evaluate constant string expressions.
This includes strings with lists, dicts and tuples using the abstract syntax tree created by ``compiler.parse``.
.. deprecated:: 1.10.0
See Also -------- safe_eval
""" # 2014-10-15, 1.10 warnings.warn("SafeEval is deprecated in 1.10 and will be removed.", DeprecationWarning, stacklevel=2)
cls = node.__class__ meth = getattr(self, 'visit' + cls.__name__, self.default) return meth(node)
raise SyntaxError("Unsupported source construct: %s" % node.__class__)
return self.visit(node.body)
return node.n
return node.s
return node.s
return dict([(self.visit(k), self.visit(v)) for k, v in zip(node.keys, node.values)])
return tuple([self.visit(i) for i in node.elts])
return [self.visit(i) for i in node.elts]
import ast if isinstance(node.op, ast.UAdd): return +self.visit(node.operand) elif isinstance(node.op, ast.USub): return -self.visit(node.operand) else: raise SyntaxError("Unknown unary op: %r" % node.op)
if node.id == 'False': return False elif node.id == 'True': return True elif node.id == 'None': return None else: raise SyntaxError("Unknown name: %s" % node.id)
return node.value
""" Protected string evaluation.
Evaluate a string containing a Python literal expression without allowing the execution of arbitrary non-literal code.
Parameters ---------- source : str The string to evaluate.
Returns ------- obj : object The result of evaluating `source`.
Raises ------ SyntaxError If the code has invalid Python syntax, or if it contains non-literal code.
Examples -------- >>> np.safe_eval('1') 1 >>> np.safe_eval('[1, 2, 3]') [1, 2, 3] >>> np.safe_eval('{"foo": ("bar", 10.0)}') {'foo': ('bar', 10.0)}
>>> np.safe_eval('import os') Traceback (most recent call last): ... SyntaxError: invalid syntax
>>> np.safe_eval('open("/home/user/.ssh/id_dsa").read()') Traceback (most recent call last): ... SyntaxError: Unsupported source construct: compiler.ast.CallFunc
""" # Local import to speed up numpy's import time.
""" Utility function to check median result from data for NaN values at the end and return NaN in that case. Input result can also be a MaskedArray.
Parameters ---------- data : array Input data to median function result : Array or MaskedArray Result of median function axis : {int, sequence of int, None}, optional Axis or axes along which the median was computed. out : ndarray, optional Output array in which to place the result. Returns ------- median : scalar or ndarray Median or NaN in axes which contained NaN in the input. """ return result # masked NaN values are ok warnings.warn("Invalid value encountered in median", RuntimeWarning, stacklevel=3) if out is not None: out[...] = data.dtype.type(np.nan) result = out else: result = data.dtype.type(np.nan) warnings.warn("Invalid value encountered in median for" + " %d results" % np.count_nonzero(n.ravel()), RuntimeWarning, stacklevel=3) result[n] = np.nan
#----------------------------------------------------------------------------- |