Source code for climextRemes_wrapper

"""
.. module:: climextRemes
   :platform: Unix, Mac, Windows
   :synopsis: Python wrapper for the climextRemes package.

.. moduleauthor:: Christopher Paciorek <paciorek@berkeley.edu>

"""

version = ""
Fort = None

# As of rpy2 >= 3.0.0, use of NULLType rather than RNULLType
import rpy2.rinterface

if hasattr(rpy2.rinterface, 'NULLType'):
    NULLType = rpy2.rinterface.NULLType   # rpy2 >= 3.0.0
else:
    NULLType = rpy2.rinterface.RNULLType  # rpy2 < 3.0.0

[docs] def compute_input_map(input_arg_map): import rpy2 import numpy import rpy2.robjects.numpy2ri if isinstance(input_arg_map, NULLType): #result = {} #result[name] = None return None # As of rpy2 >= 3.0.0, return elements of list are numpy arrays not R vectors if isinstance(input_arg_map, numpy.ndarray): return input_arg_map # don't change RObject if isinstance(input_arg_map, rpy2.robjects.RObject): #result = {} #result[name] = input_arg_map return input_arg_map # named array if isinstance(input_arg_map, rpy2.robjects.vectors.ListVector): output_names = [] output_values = [] try: for (i,xname) in enumerate(input_arg_map.names): try: value = compute_input_map(input_arg_map[i]) output_names.append(xname) output_values.append(value) #print xname, type(input_arg_map[i]), value except: output_names.append(xname) output_values.append("Compute Error") except: output_names.append("Error") output_values.append("Error") result = dict() for (i,f) in enumerate(output_names): if isinstance(output_values[i], dict): if "__vector" in output_values[i]: result[f + "_names"] = output_values[i]["__vector_names"] result[f] = output_values[i]["__vector"] name_list = result[f + "_names"].tolist() if isinstance(name_list, NULLType): #result[f + "_names"] = None del result[f + "_names"] else: res = result[f + "_names"] for j in range(len(res)): if isinstance(res[j], NULLType): res[j] = None elif "__dict" in output_values[i]: if "__dict_row_names" in output_values[i]: result[f + "_row_names"] = output_values[i]["__dict_row_names"] name_list = result[f + "_row_names"].tolist() if isinstance(name_list, NULLType): #result[f + "_row_names"] = None del result[f + "_row_names"] else: res = result[f + "_row_names"] for j in range(len(res)): if isinstance(res[j], NULLType): res[j] = None if "__dict_column_names" in output_values[i]: result[f + "_column_names"] = output_values[i]["__dict_column_names"] name_list = result[f + "_column_names"].tolist() if isinstance(name_list, NULLType): #result[f + "_column_names"] = None del result[f + "_column_names"] else: res = result[f + "_column_names"] for j in range(len(res)): if isinstance(res[j], NULLType): res[j] = None if "__dict_dimnames" in output_values[i]: for (i2, f2) in enumerate(output_values[i]["__dict_dimnames"]): result[f + "_dim" + str(i2+1) + "_names"] = f2 try: name_list = result[f + "_dim" + str(i2+1) + "_names"].tolist() except: name_list = None if name_list is None or isinstance(name_list, NULLType): #result[f + "_column_names"] = None del result[f + "_dim" + str(i2+1) + "_names"] else: res = result[f + "_dim" + str(i2+1) + "_names"] for j in range(len(res)): if isinstance(res[j], NULLType): res[j] = None result[f] = output_values[i]["__dict"] else: result[f] = output_values[i] else: result[f] = output_values[i] return result # put Array and Matrix before Vectors as they also are Vectors and # want special handling specific to Array and Matrix if isinstance(input_arg_map, rpy2.robjects.vectors.Matrix): result = {} name = "__dict" result[name] = numpy.array(input_arg_map) try: result[name + "_row_names"] = numpy.array(input_arg_map.rownames) except: pass try: result[name + "_column_names"] = numpy.array(input_arg_map.colnames) except: pass return result if isinstance(input_arg_map, rpy2.robjects.vectors.Array): result = {} name = "__dict" result[name] = numpy.array(input_arg_map) result[name + "_dimnames"] = [] for (i,f) in enumerate(input_arg_map.dimnames): result[name + "_dimnames"].append(compute_input_map(f)) return result # other vectors if isinstance(input_arg_map, rpy2.robjects.vectors.IntVector): result = {} name = "__vector" input_arg_map_save = input_arg_map try: result[name+"_names"] = numpy.array(input_arg_map.names) except: pass has_nan = False for f in input_arg_map: if f is rpy2.rinterface.NA_Integer: has_nan = True break if has_nan: input_arg_map = [numpy.nan if f is rpy2.robjects.NA_Integer else f for f in input_arg_map] result[name] = numpy.array(input_arg_map, numpy.float) else: result[name] = numpy.array(input_arg_map) if name+"_names" not in result.keys() or isinstance(input_arg_map_save.names, NULLType): result = result[name] return result if isinstance(input_arg_map, rpy2.robjects.vectors.FloatVector): result = {} name = "__vector" try: result[name+"_names"] = numpy.array(input_arg_map.names) except: pass # Float correctly handles numpy.nan conversion result[name] = numpy.array(input_arg_map) if name+"_names" not in result.keys() or isinstance(input_arg_map.names, NULLType): result = result[name] return result if isinstance(input_arg_map, rpy2.robjects.vectors.StrVector): result = {} name = "__vector" try: result[name+"_names"] = numpy.array(input_arg_map.names) except: pass try: result[name] = numpy.array(input_arg_map) except: result[name] = input_arg_map if name+"_names" not in result.keys() or isinstance(input_arg_map.names, NULLType): result = result[name] return result if isinstance(input_arg_map, rpy2.robjects.vectors.BoolVector): result = {} name = "__vector" input_arg_map_save = input_arg_map try: result[name+"_names"] = numpy.array(input_arg_map.names) except: pass has_nan = False for f in input_arg_map: if f is rpy2.rinterface.NA_Logical: has_nan = True break if has_nan: input_arg_map = [numpy.nan if f is rpy2.robjects.NA_Logical else f for f in input_arg_map] result[name] = numpy.array(input_arg_map, numpy.float) else: result[name] = numpy.array(input_arg_map) if name+"_names" not in result.keys() or isinstance(input_arg_map_save.names, NULLType): result = result[name] return result
""" def compute_input_map(input_arg_map): import rpy2 input_map = None if isinstance(input_arg_map, rpy2.rinterface.RNULLType): input_map = None elif isinstance(input_arg_map, rpy2.robjects.vectors.ListVector): input_map = [] try: for (i,name) in enumerate(input_arg_map.names): try: value = input_arg_map[i] #print i, name, type(value), isinstance(value, rpy2.robjects.vectors.Vector) if isinstance(value, rpy2.robjects.vectors.ListVector): input_map.append( (name, compute_input_map(value)) ) elif isinstance(value, rpy2.robjects.vectors.Vector): input_map.append((name,value[0])) elif isinstance(value, rpy2.rinterface.RNULLType): input_map.append((name,None)) else: input_map.append((name,None)) except: input_map.append((name,None)) except: print "unable to parse", str(input_arg_map) elif isinstance(input_arg_map, rpy2.robjects.vectors.Vector): input_map = [] for v in input_arg_map: result = compute_input_map(v) input_map.append(result) elif isinstance(input_arg_map, rpy2.robjects.RObject): input_map = input_arg_map # TODO handle this case.. else: # what else is there? input_map = input_arg_map return input_map """ def __initialize_wrapper(): global version, Fort import numpy import pandas import rpy2 import rpy2.robjects as robjects import rpy2.robjects.help as rh from rpy2.robjects import numpy2ri from rpy2.robjects import pandas2ri from rpy2.robjects.packages import importr import fnmatch import os import re # rpy2.robjects.activate() if int(rpy2.__version__.split('.')[0]) < 3: pandas2ri.activate() numpy2ri.activate() root_dir = os.path.dirname(os.path.realpath(__file__)) __extRemes__ = importr("extRemes") __climextRemes__ = importr("climextRemes") __climextRemesHelp__ = rh.Package("climextRemes") __version__ = robjects.r(''' packageVersion("climextRemes") ''')[0] __version__ = ".".join([str(f) for f in __version__]) version = __version__ Fort = robjects.r(''' data(Fort) ord <- order(Fort$year, Fort$month, Fort$day) Fort <- Fort[ord, ] ''') if int(rpy2.__version__.split('.')[0]) >= 3: with rpy2.robjects.conversion.localconverter(rpy2.robjects.default_converter + rpy2.robjects.pandas2ri.converter): Fort = rpy2.robjects.conversion.rpy2py(Fort) else: Fort = pandas.DataFrame(Fort) examples = {} examples_dir = "{0}/../examples".format(root_dir) for file in os.listdir(examples_dir): if fnmatch.fnmatch(file, '*_examples.py'): filename = examples_dir + "/" + file with open(filename, "r") as infile: key = file.replace("_examples.py", "") value = infile.read() examples[key] = value arguments_dir = "{0}/../python_help".format(root_dir) for file in os.listdir(arguments_dir): if fnmatch.fnmatch(file, '*_args.txt'): filename = arguments_dir + "/" + file with open(filename, "r") as infile: key = file.replace("_args.txt", "") value = infile.read() examples[key + "_arguments"] = value #print("examples", examples.keys()) class climextRemesReturnObject(object): def __init__(self): pass def __repr__(self): return str(self.__dict__.keys()) def __parseResult(obj): result = None if hasattr(obj, 'names') == False: return obj #print obj.names, rpy2.rinterface.NULL, type(obj), rpy2.rinterface.RNULLType if obj.names is rpy2.rinterface.NULL or \ type(obj.names) is NULLType or \ (len(obj.names) == 1 and obj.names[0].replace(".","").isdigit()): if isinstance(obj, robjects.Vector) and len(obj) == 1: result = obj[0] else: result = robjects.conversion.ri2py(obj) elif isinstance(obj, robjects.Vector): result = climextRemesReturnObject() result.names = numpy.array(obj.names) for i in range(len(obj.names)): #print obj.names[i] result.__dict__[obj.names[i] + "_r"] = numpy.array(obj[i]) result.__dict__[obj.names[i]] = __parseResult(obj[i]) return result def __climextRemesWrapFunction(method_name, override_examples): names = [] defaults = [] signature = robjects.r(''' library(climextRemes) as.list(args({0})) '''.format(method_name)) def quote_args(text, arg_names): text = re.sub("( " + " | ".join(arg_names) + " )", "'\\1'", text) # As of 0.2.1 changed from curly to straight quote to avoid this error in Py 2.7: # SyntaxError: Non-ASCII character '\xe2' in file /accounts/gen/vis/paciorek/R/x86_64-pc-linux-gnu-library/3.5/climextRemes/python/climextRemes_wrapper.py on line 317, but no encoding declared; see http://python.org/dev/peps/pep-0263/ for details # This is causing extra spaces because can't tell left vs right single quote, so remove until we go back to curly quotes. # text = text.replace("' ", "'") # text = text.replace(" '", "'") return(text) for (i,name) in enumerate(signature.names): if len(name) > 0: name = name.replace(".","_") names.append(name) try: d = signature[i][0] if isinstance(d, rpy2.robjects.robject.RObject) or isinstance(d, rpy2.rinterface.SexpSymbol): defaults.append(None) else: defaults.append(d) except: defaults.append(None) gdoc = __climextRemesHelp__.fetch(method_name) ## As of rpy2 >= 3.4.0 need \\ in key names use_backslash = True if '\\title' in gdoc.sections.keys() else False key_names = ['title', 'description'] if use_backslash: key_names = ['\\' + nm for nm in key_names] gdoc_help = gdoc.to_docstring(key_names) if method_name + "_arguments" in override_examples: new_arguments = override_examples[method_name + "_arguments"] arguments = new_arguments.split("@param ") new_arguments = "arguments\n" new_arguments += "---------\n" argument_names = [] for arg in arguments[1:]: n_arg = arg.split(" ") argument_names.append(n_arg[0]) n_arg[0] = n_arg[0] + ":" arg = " ".join(n_arg) new_arguments += arg + "\n" #new_arguments = new_arguments.replace("@param ", "") #gdoc_help += "arguments\n" #gdoc_help += "----------\n" #gdoc_help += new_arguments #.replace("\n", "\n\n") #gdoc_help.replace("\n\ndetails\n", "\n" + new_arguments + "\n\ndetails\n") gdoc_help += new_arguments else: key_name = '\\arguments' if use_backslash else 'arguments' gdoc_arguments = gdoc.to_docstring([key_name]) res = gdoc_arguments.split("\n") output = "" argument_names = [] for r in res: r2 = r.split() if len(r2) >= 2: argument_names.append(r2[0]) r2[0] = r2[0] + ":" r2 = " ".join(r2) output += " " + r2 + "\n" else: output += r + "\n" gdoc_help += output + "\n\n" #method = getattr(__climextRemes__, method_name) #arglist = method.formals().names help_keys = list(gdoc.sections.keys()) key_name = '\\details' if use_backslash else 'details' if key_name in help_keys: details = gdoc.to_docstring([key_name]) details = quote_args(details, argument_names) gdoc_help += details help_keys.remove(key_name) key_name = '\\value' if use_backslash else 'value' if key_name in help_keys: value = gdoc.value() if use_backslash: # value needs to be handled differently as of rpy2 >= 3.4.0 value = ' '.join(["\n\n" if v == "\n" else v.strip() for v in value[1:]]) value = "\n" + value.strip() + "\n" else: value = value.replace("\code{", "'") value = value.replace("}", "'") gdoc_help += "value\n-----\n\n" + value + "\n" help_keys.remove(key_name) if "usage" in help_keys: help_keys.remove('usage') # this is the R usage so exclude if "alias" in help_keys: help_keys.remove('alias') # this is the R alias so exclude if "arguments" in help_keys: help_keys.remove('arguments') # handled separately if "examples" in help_keys: help_keys.remove('examples') # handled separately if "name" in help_keys: help_keys.remove('name') # this is redundant so exclude if "title" in help_keys: help_keys.remove('title') # handled separately if "description" in help_keys: help_keys.remove('description') # handled separately if "\\usage" in help_keys: help_keys.remove('\\usage') # this is the R usage so exclude if "\\alias" in help_keys: help_keys.remove('\\alias') # this is the R alias so exclude if "\\arguments" in help_keys: help_keys.remove('\\arguments') # handled separately if "\\examples" in help_keys: help_keys.remove('\\examples') # handled separately if "\\name" in help_keys: help_keys.remove('\\name') # this is redundant so exclude if "\\title" in help_keys: help_keys.remove('\\title') # handled separately if "\\description" in help_keys: help_keys.remove('\\description') # handled separately others = gdoc.to_docstring(help_keys) others = quote_args(others, argument_names) gdoc_help += others if method_name in override_examples: gdoc_help += "examples\n" gdoc_help += "--------\n" gdoc_help += ">>> " + override_examples[method_name].replace("\n", "\n... ") #index = gdoc_help.find("examples") #if index >= 0: # gdoc_help = gdoc_help[0:index] # if method_name in override_examples: # gdoc_help += "examples\n" # gdoc_help += "---------\n" # gdoc_help += override_examples[method_name].replace("\n", "\n\n") # some cleanup gdoc_help = gdoc_help.replace("title\n-----", "\n", 1) # 'title' is extraneous gdoc_help = gdoc_help.replace("\n \n", "\n\n") gdoc_help = gdoc_help.replace("---\n\n\n", "---\n") gdoc_help = gdoc_help.replace("\n\n\n", "\n\n") help_keys = [hk.replace("\\", "") for hk in help_keys] help_keys.extend(["arguments", "examples", "description", "details", "value"]) for help in help_keys: # Sphinx thinks repeated characters are section titles gdoc_help = gdoc_help.replace(help + "\n" + "-"*len(help), "**" + help + "**\n") gdoc_help = gdoc_help.replace('TRUE', 'True') gdoc_help = gdoc_help.replace('FALSE', 'False') gdoc_help = gdoc_help.replace('NULL', 'None') def decorator(*args, **kwargs): import numpy new_args = [] new_kwargs = {} for a in args: if isinstance(a, dict): new_args.append(rpy2.robjects.vectors.ListVector(a)) else: if int(rpy2.__version__.split('.')[0]) >= 3 and isinstance(a, numpy.ndarray): # new_args.append(rpy2.robjects.vectors.FloatVector(a) with rpy2.robjects.conversion.localconverter(rpy2.robjects.default_converter + rpy2.robjects.numpy2ri.converter): new_args.append(rpy2.robjects.conversion.py2rpy(a)) elif int(rpy2.__version__.split('.')[0]) >= 3 and isinstance(a, pandas.core.frame.DataFrame): with rpy2.robjects.conversion.localconverter(rpy2.robjects.default_converter + rpy2.robjects.pandas2ri.converter): new_args.append(rpy2.robjects.conversion.py2rpy(a)) else: if a is None: a = rpy2.rinterface.NULL # rpy2 doesn't convert scalar numpy ints or floats. if isinstance(a, (numpy.floating, numpy.integer)): a = float(a) new_args.append(a) for b in kwargs.keys(): if isinstance(kwargs[b], dict): new_kwargs[b] = rpy2.robjects.vectors.ListVector(kwargs[b]) else: if int(rpy2.__version__.split('.')[0]) >= 3 and isinstance(kwargs[b], numpy.ndarray): with rpy2.robjects.conversion.localconverter(rpy2.robjects.default_converter + rpy2.robjects.numpy2ri.converter): new_kwargs[b] = rpy2.robjects.conversion.py2rpy(kwargs[b]) elif int(rpy2.__version__.split('.')[0]) >= 3 and isinstance(kwargs[b], pandas.core.frame.DataFrame): with rpy2.robjects.conversion.localconverter(rpy2.robjects.default_converter + rpy2.robjects.pandas2ri.converter): new_kwargs[b] = rpy2.robjects.conversion.py2rpy(kwargs[b]) else: if b is None: b = rpy2.rinterface.NULL # rpy2 doesn't convert scalar numpy ints or floats. if isinstance(b, (numpy.floating, numpy.integer)): b = float(b) new_kwargs[b] = kwargs[b] new_kwargs[b] = kwargs[b] method = getattr(__climextRemes__, method_name) retobj = method(*new_args, **new_kwargs) #return __parseResult(retobj) return compute_input_map(retobj) decorator.__doc__ = gdoc_help decorator.__name__ = method_name + "_" decorator.__names__ = names decorator.__defaults__ = tuple(defaults) argstr = ", ".join(names) fakefunc = "def %s(%s):\n return %s(%s)\n" % (method_name, argstr, method_name + "_", argstr) fakefunc_code = compile(fakefunc, "fakesource", "exec") fakeglobals = {} eval(fakefunc_code, {method_name + "_": decorator}, fakeglobals) f_with_good_sig = fakeglobals[method_name] f_with_good_sig.__doc__ = gdoc_help f_with_good_sig.__name__ = method_name f_with_good_sig.__defaults__ = tuple(defaults) return f_with_good_sig for __i__ in __climextRemes__._exported_names: result = __climextRemesWrapFunction(__i__, examples) globals()[__i__] = result __initialize_wrapper()