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


[docs]def compute_input_map(input_arg_map): import rpy2 import numpy import rpy2.robjects.numpy2ri # NULL turns into None if isinstance(input_arg_map, rpy2.rinterface.RNULLType): #result = {} #result[name] = None return None # 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, rpy2.rinterface.RNULLType): #result[f + "_names"] = None del result[f + "_names"] else: res = result[f + "_names"] for j in range(len(res)): if isinstance(res[j],rpy2.rinterface.RNULLType): res[j] = None elif "__dict" in output_values[i]: result[f + "_row_names"] = output_values[i]["__dict_row_names"] result[f + "_column_names"] = output_values[i]["__dict_column_names"] name_list = result[f + "_row_names"].tolist() if isinstance(name_list, rpy2.rinterface.RNULLType): #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],rpy2.rinterface.RNULLType): res[j] = None name_list = result[f + "_column_names"].tolist() if isinstance(name_list, rpy2.rinterface.RNULLType): #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],rpy2.rinterface.RNULLType): res[j] = None result[f] = output_values[i]["__dict"] else: result[f] = output_values[i] else: result[f] = output_values[i] 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, rpy2.rinterface.RNULLType): 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, rpy2.rinterface.RNULLType): 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 result[name] = numpy.array(input_arg_map) if name+"_names" not in result.keys() or isinstance(input_arg_map.names, rpy2.rinterface.RNULLType): 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, rpy2.rinterface.RNULLType): result = result[name] return result if isinstance(input_arg_map, rpy2.robjects.vectors.Matrix): output_col_names = numpy.array(input_arg_map.colnames) output_row_names = numpy.array(input_arg_map.rownames) result = {} name = "__dict" result[name] = numpy.array(input_arg_map) result[name + "_row_names"] = output_row_names result[name + "_column_names"] = output_col_names 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 import rpy2.robjects.numpy2ri as numpy2ri from rpy2.robjects.packages import importr import fnmatch import os import re from rpy2.robjects import pandas2ri #rpy2.robjects.activate() 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 = pandas.DataFrame(robjects.r(''' data(Fort) ord <- order(Fort$year, Fort$month, Fort$day) Fort <- Fort[ord, ] ''')) 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 rpy2.rinterface.RNULLType 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) 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): defaults.append(None) else: defaults.append(d) except: defaults.append(None) gdoc = __climextRemesHelp__.fetch(method_name) gdoc_help = gdoc.to_docstring(['title', 'description']) 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: gdoc_arguments = gdoc.to_docstring(["arguments"]) 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()) if "details" in help_keys: details = gdoc.to_docstring(["details"]) details = quote_args(details, argument_names) gdoc_help += details help_keys.remove('details') if "value" in help_keys: value = gdoc.value() value = value.replace("\code{", "‘") value = value.replace("}", "’") gdoc_help += "value\n-----\n\n" + value + "\n" help_keys.remove('value') 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.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): #print kwargs, args new_args = [] new_kwargs = {} for a in args: if isinstance(a, dict): new_args.append(rpy2.robjects.vectors.ListVector(a)) else: if a is None: a = rpy2.rinterface.NULL 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 b is None: b = rpy2.rinterface.NULL 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()