Exemple #1
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def classify_encapsulated(audio_summary, track_info, pickle_file):
	"""Performs a similar operation to classify() and all the above functions in one step
	But retrieves fit from pickle, for the GUI
	"""
	f = open(pickle_file, 'r')
	fit = pickle.load(f)
	f.close()
	rv = {}
	#print track_info.keys()
	#print track_info[audio_summary]['title'].keys()
	rv["speechiness"] = [audio_summary['audio_summary']['speechiness']]
	rv["time_sig"] = [audio_summary['audio_summary']['time_signature']]
	rv["bpm"] = [audio_summary['audio_summary']['tempo']]
	rv["key"] = [audio_summary['audio_summary']['key']]
	rv["duration"] = [audio_summary['audio_summary']['duration']]
	rv["loudness"] = [audio_summary['audio_summary']['loudness']]
	rv["end_of_fade_in"] = [track_info['track']['end_of_fade_in']]
	rv["start_of_fade_out"] = [track_info['track']['start_of_fade_out']]
	rv["bpm_range"] = [proc.bpm_range(track_info['beats'])]
	rv["max_bpm_spike"] = [proc.max_bpm_spike(track_info['beats'])]
	try:
		rv["num_keys"] = [proc.num_keys(track_info['sections'])]
	except:
		rv["num_keys"] = [1]
	rv["sections"] = [proc.num_sections(track_info['sections'])]
	new_df = build_data_frame([rv],["Unknown"])
	p = prob_category(new_df,fit)
	robjects.globalenv["pred"] = p
	edm_prob = robjects.default_ri2py(p.rx(1))[0]
	folk_prob = robjects.default_ri2py(p.rx(2))[0]
	rap_prob = robjects.default_ri2py(p.rx(3))[0]
	cls = classify(new_df,fit)
	return [(edm_prob,folk_prob,rap_prob),cls[0]]
Exemple #2
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 def custom_ri2py(obj):
    res = robjects.default_ri2py(obj)
    
    if isinstance(res, robjects.Vector) and (len(res) == 1):
        res = super(robjects.vectors.Vector, res).__getitem__(0)
        
        if isinstance(res, rinterface.Sexp):
            res = robjects.default_ri2py(res)
            
    return res
Exemple #3
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def get_sd_ratios(what,orgn,dstn,fltnum,dfrom,dto,daysprior,cls):

    curr_dt = datetime.now()
    curr_date = date(curr_dt.year, curr_dt.month, curr_dt.day)

    if what == 'pb':
        [vals,obs,diff,dptdts] = get_fcsterr_by_dptdt_dflc_lvl('uncons',orgn,dstn,fltnum,dfrom,curr_date,daysprior,cls)
    elif what == 'fb':
        print "fp parameter what isn't implemented"
        assert 0
    elif what == 'ns':
        vals = get_noshows_by_flc_lvl(orgn,dstn,fltnum,dfrom,dto,cls)
    else:
        print 'Unknown parameter what in get_sd_ratios'
        assert 0

    print vals

    try:

        vals_r = robjects.FloatVector(vals)
        res_r = r.find_var_prop(vals_r) 
        res = robjects.default_ri2py(res_r)   
    except:
        res = [0,0]

    return res
Exemple #4
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def ks_p_value(l):

    r_l = robjects.IntVector(l)
    r_p_value = r.get_ks_p_value(r_l)
    p_value = robjects.default_ri2py(r_p_value)[0]

    return p_value
Exemple #5
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def cramer_von_mises_p_value(l):

    r_l = robjects.IntVector(l)
    r_p_value = r.get_cr_von_mis_p_value(r_l)
    p_value = robjects.default_ri2py(r_p_value)[0]

    return p_value
Exemple #6
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 def as_dendropy_object(o, taxon_set=None):
     """
     Returns a DendroPy object corresponding to the ape object ``o``. If ``o`` is
     a single tree (i.e., ``phylo``), then a DendroPy Tree is returned. If ``o`` is
     a list of trees (i.e., a ``multiPhylo`` object, or list of ``phylo`` objects),
     then a DendroPy TreeList is returned.
     """
     if o.rclass[0] == "multiPhylo":
         f = tempfile.NamedTemporaryFile()
         _R["write.nexus"](o, file=f.name)
         return dendropy.TreeList.get_from_path(f.name, "nexus", taxon_set=taxon_set)
     elif o.rclass[0] == "phylo":
         f = tempfile.NamedTemporaryFile()
         _R["write.nexus"](o, file=f.name)
         return dendropy.Tree.get_from_path(f.name, "nexus", taxon_set=taxon_set)
     elif o.rclass[0] == "list":
         f = tempfile.NamedTemporaryFile()
         _R["write.nexus.data"](o, file=f.name)
         #        print open(f.name, "r").read()
         d = dendropy.DataSet.get_from_path(f.name, "nexus", taxon_set=taxon_set)
         if len(d.char_matrices) == 0:
             raise ValueError("No character data found")
         elif len(d.char_matrices) == 1:
             return d.char_matrices[0]
         else:
             raise ValueError("Multiple character matrices returned")
     else:
         return robjects.default_ri2py(o)
Exemple #7
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def ri2pandas(o):
    if isinstance(o, DataFrame):
        raise NotImplementedError(
            "Conversion from rpy2 DataFrame to pandas' DataFrame")
    else:
        res = ro.default_ri2py(o)
    return res
Exemple #8
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 def as_dendropy_object(o, taxon_set=None):
     """
     Returns a DendroPy object corresponding to the ape object ``o``. If ``o`` is
     a single tree (i.e., ``phylo``), then a DendroPy Tree is returned. If ``o`` is
     a list of trees (i.e., a ``multiPhylo`` object, or list of ``phylo`` objects),
     then a DendroPy TreeList is returned.
     """
     if o.rclass[0] == "multiPhylo":
         f = tempfile.NamedTemporaryFile()
         _R['write.nexus'](o, file=f.name)
         return dendropy.TreeList.get_from_path(f.name,
                                                "nexus",
                                                taxon_set=taxon_set)
     elif o.rclass[0] == "phylo":
         f = tempfile.NamedTemporaryFile()
         _R['write.nexus'](o, file=f.name)
         return dendropy.Tree.get_from_path(f.name,
                                            "nexus",
                                            taxon_set=taxon_set)
     elif o.rclass[0] == "list":
         f = tempfile.NamedTemporaryFile()
         _R['write.nexus.data'](o, file=f.name)
         #        print open(f.name, "r").read()
         d = dendropy.DataSet.get_from_path(f.name,
                                            "nexus",
                                            taxon_set=taxon_set)
         if len(d.char_matrices) == 0:
             raise ValueError("No character data found")
         elif len(d.char_matrices) == 1:
             return d.char_matrices[0]
         else:
             raise ValueError("Multiple character matrices returned")
     else:
         return robjects.default_ri2py(o)
Exemple #9
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def get_fcsterr_mse(type, orgn, dstn, fltnum, dfrom, dto, daysprior, cls):

    [fcst, obs, diff, dptdt_l] = get_fcsterr_by_dptdt_dflc_lvl(type, orgn, dstn, fltnum, dfrom, dto, daysprior, cls)
    r_diff = robjects.FloatVector(diff)
    r_mse = r.get_mse(r_diff)
    mse = robjects.default_ri2py(r_mse)[0]

    return mse
Exemple #10
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def ri2numpy(o):
    if isinstance(o, ListVector):
        res = numpy.rec.fromarrays(o, names=tuple(o.names))
    elif isinstance(o, Vector) and (type(o) != Vector):
        res = numpy.asarray(o)
    else:
        res = ro.default_ri2py(o)
    return res
 def f(obj):
     pyobj = robjects.default_ri2py(obj)
     inherits = rinterface.baseenv["inherits"]
     classname = rinterface.SexpVector(["density", ], 
                                       rinterface.STRSXP)
     if inherits(pyobj, classname)[0]:
         pyobj = Density(pyobj)
     return pyobj
Exemple #12
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def ri2numpy(o):
    if isinstance(o, ListVector):
        res = numpy.rec.fromarrays(o, names=tuple(o.names))
    elif isinstance(o, Vector) and (type(o) != Vector):
        res = numpy.asarray(o)
    else:
        res = ro.default_ri2py(o)
    return res
 def testMapperR2Python_s4(self):
     robjects.r('setClass("A", representation(x="integer"))')
     classname = rinterface.StrSexpVector(["A", ])
     one = rinterface.IntSexpVector([1, ])
     sexp = rinterface.globalenv.get("new")(classname, 
                                            x=one)
     self.assertTrue(isinstance(robjects.default_ri2py(sexp), 
                                robjects.RS4))
Exemple #14
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def shapiro_wilk_p_value(l):

    # l = list(Set(l))
    r_l = robjects.FloatVector(l)
    r_p_value = r.get_shapiro_wilk_p_value(r_l)
    p_value = robjects.default_ri2py(r_p_value)[0]

    return p_value
Exemple #15
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 def f(obj):
     pyobj = robjects.default_ri2py(obj)
     inherits = rinterface.baseenv["inherits"]
     classname = rinterface.SexpVector([
         "density",
     ], rinterface.STRSXP)
     if inherits(pyobj, classname)[0]:
         pyobj = Density(pyobj)
     return pyobj
Exemple #16
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def convert_xts_to_df(o):
    """
        Will convert xts objects to DataFrame
    """
    dates = o.do_slot('index')
    index = convert_posixct_to_index(dates)
    res = robjects.default_ri2py(o)
    df = _convert_Matrix(res)
    df.index = index
    return df
Exemple #17
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def convert_xts_to_df(o):
    """
        Will convert xts objects to DataFrame
    """
    dates = o.do_slot('index')
    dates = np.array(dates, dtype=np.dtype("M8[s]"))
    res = robjects.default_ri2py(o)
    df = rcom.convert_robj(res)
    df.index = dates
    return df
Exemple #18
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def get_ljung_box_pval(type, orgn, dstn, fltnum, dfrom, dto, daysprior, cls):

    [fcst, obs, diff, dptdt_l] = get_fcsterr_by_dptdt_dflc_lvl(type, orgn, dstn, fltnum, dfrom, dto, daysprior, cls)
    if len(diff) != 0:
        r_diff = robjects.FloatVector(diff)
        r_pval = r.get_ljung_box_pval(r_diff)
        pval = robjects.default_ri2py(r_pval)[0]
    else:
        pval = 0
    return pval
Exemple #19
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def convert_xts_to_df(o):
    """
        Will convert xts objects to DataFrame
    """
    dates = o.do_slot('index')
    dates = np.array(dates, dtype=np.dtype("M8[s]"))
    res = robjects.default_ri2py(o)
    df = rcom.convert_robj(res)
    df.index = dates
    return df
Exemple #20
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 def testMapperR2Python_s4(self):
     robjects.r('setClass("A", representation(x="integer"))')
     classname = rinterface.StrSexpVector([
         "A",
     ])
     one = rinterface.IntSexpVector([
         1,
     ])
     sexp = rinterface.globalenv.get("new")(classname, x=one)
     self.assertTrue(isinstance(robjects.default_ri2py(sexp), robjects.RS4))
Exemple #21
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def my_ri2py(o):
    res = None
    try:
        rcls = o.do_slot("class")
    except LookupError:
        rcls = [None]

    if isinstance(o, ri.SexpVector):
        if 'xts' in rcls:
            res = convert_xts_to_df(o)

    if res is None:
        res = robjects.default_ri2py(o)

    return res
Exemple #22
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def get_esp_params(flights,dows,sh_id,pool_ids,clss):

    sizes = []
    alphas = []

    for flight in flights:

        orgn = flight[0]
        dstn = flight[1]
        fltnum = flight[2]

        sh = splitHistory(sh_id)

        for dow in dows:

            for pool_id in pool_ids:

                for cls in clss:

                    for daysprior in get_dayspriors(): 

                        fdr = fcstDataReader(orgn,dstn,fltnum,\
                                             cls,daysprior,dow,sh)
                        vals = fdr.get_fcst_minus_booked_vals('uncons',pool_id)
                        sample_size = get_sample_size(vals)

                        if sample_size is not None:

                            sizes.append(sample_size)
                            vals_r = robjects.FloatVector(vals)
                            vals_r_ts = r.ts(vals_r,frequency=len(vals))
                            hw_res = r.HoltWinters(vals_r,beta=False,gamma=False)
                            alpha = robjects.default_ri2py(hw_res[2])
                            alphas.append(alpha)

    lag = int(ceil(mean(sizes)))
    alpha = float(mean(alphas))

    return [lag, alpha]
Exemple #23
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def ri2py_list(obj):
    if 'data.frame' in obj.rclass:
        # R "factor" vectors will not convert well by default
        # (will become integers), so we build a temporary list o2
        # with the factors as strings.
        o2 = list()
        # An added complication is that the conversion defined
        # in this module will make __getitem__ at the robjects
        # level return numpy arrays
        for column in rinterface.ListSexpVector(obj):
            if 'factor' in column.rclass:
                levels = tuple(column.do_slot("levels"))
                column = tuple(levels[x-1] for x in column)
            o2.append(column)
        names = obj.do_slot('names')
        if names is NULL:
            res = numpy.rec.fromarrays(o2)
        else:
            res = numpy.rec.fromarrays(o2, names=tuple(names))
    else:
        # not a data.frame, yet is it still possible to convert it
        res = ro.default_ri2py(obj)
    return res
Exemple #24
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def ri2py_list(obj):
    if 'data.frame' in obj.rclass:
        # R "factor" vectors will not convert well by default
        # (will become integers), so we build a temporary list o2
        # with the factors as strings.
        o2 = list()
        # An added complication is that the conversion defined
        # in this module will make __getitem__ at the robjects
        # level return numpy arrays
        for column in rinterface.ListSexpVector(obj):
            if 'factor' in column.rclass:
                levels = tuple(column.do_slot("levels"))
                column = tuple(levels[x-1] for x in column)
            o2.append(column)
        names = obj.do_slot('names')
        if names is NULL:
            res = numpy.rec.fromarrays(o2)
        else:
            res = numpy.rec.fromarrays(o2, names=tuple(names))
    else:
        # not a data.frame, yet is it still possible to convert it
        res = ro.default_ri2py(obj)
    return res
    def run_test(self):
        ''' take the R globalEnv located HyperGParam obj and run 
	  		HyperGTest, returns the HyperGResult obj '''

        return rob.default_ri2py(rob.r.hyperGTest(rob.r[self.par_name]))
Exemple #26
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def pd_ri2py(o):
    res = None
    try:
        rcls = o.do_slot("class")
    except LookupError, le:
        rcls = [None]

    if isinstance(o, SexpVector):
        if 'xts' in rcls:
            print 'xts'
            res = convert_xts_to_df(o)
        if 'POSIXct' in rcls:
            res = convert_posixct_to_index(o)

    if res is None:
        res = robjects.default_ri2py(o)

    return res

def convert_xts_to_df(o):
    """
        Will convert xts objects to DataFrame
    """
    dates = o.do_slot('index')
    dates = np.array(dates, dtype=np.dtype("M8[s]"))
    res = robjects.default_ri2py(o)
    df = rcom.convert_robj(res)
    df.index = dates
    return df

def convert_posixct_to_index(o):
Exemple #27
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baseenv_ri = rinterface.baseenv
globalenv_ri = rinterface.globalenv

def my_ri2py(o):
    res = None
    try:
        rcls = o.do_slot("class")
    except LookupError, le:
        rcls = [None]

    if isinstance(o, SexpVector):
        if 'xts' in rcls:
            res = convert_xts_to_df(o)

    if res is None:
        res = robjects.default_ri2py(o)

    return res

def convert_xts_to_df(o):
    """
        Will convert xts objects to DataFrame
    """
    dates = o.do_slot('index')
    dates = np.array(dates, dtype=np.dtype("M8[s]"))
    res = robjects.default_ri2py(o)
    df = rcom.convert_robj(res)
    df.index = dates
    return df

robjects.conversion.ri2py = my_ri2py
Exemple #28
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def ri2py_sexp(obj):
    if (obj.typeof in _vectortypes) and (obj.typeof != VECSXP):
        res = numpy.asarray(obj)
    else:
        res = ro.default_ri2py(obj)
    return res
Exemple #29
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	def run_test(self):
		''' take the R globalEnv located HyperGParam obj and run 
	  		HyperGTest, returns the HyperGResult obj '''
		
		return rob.default_ri2py(rob.r.hyperGTest(rob.r[self.par_name]))
Exemple #30
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 def testMapperR2Python_string(self):
     sexp = rinterface.globalEnv.get("letters")
     ob = robjects.default_ri2py(sexp)
     self.assertTrue(isinstance(ob, 
                                robjects.RVector))
 def testMapperR2Python_environment(self):
     sexp = rinterface.globalenv.get(".GlobalEnv")
     self.assertTrue(isinstance(robjects.default_ri2py(sexp), 
                                robjects.Environment))
 def testMapperR2Python_function(self):
     sexp = rinterface.globalenv.get("plot")
     ob = robjects.default_ri2py(sexp)
     self.assertTrue(isinstance(ob, 
                                robjects.Function))
 def testMapperR2Python_boolean(self):
     sexp = rinterface.globalenv.get("T")
     ob = robjects.default_ri2py(sexp)
     self.assertTrue(isinstance(ob, 
                                robjects.Vector))
Exemple #34
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def ri2py_sexp(obj):
    if (obj.typeof in _vectortypes) and (obj.typeof != VECSXP):
        res = numpy.asarray(obj)
    else:
        res = ro.default_ri2py(obj)
    return res
Exemple #35
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def ri2pandas(o):
    if isinstance(o, DataFrame):
        raise NotImplementedError("Conversion from rpy2 DataFrame to pandas' DataFrame")
    else:
        res = ro.default_ri2py(o)
    return res
Exemple #36
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 def testMapperR2Python_boolean(self):
     sexp = rinterface.globalenv.get("T")
     ob = robjects.default_ri2py(sexp)
     self.assertTrue(isinstance(ob, robjects.Vector))
Exemple #37
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 def testMapperR2Python_environment(self):
     sexp = rinterface.globalenv.get(".GlobalEnv")
     self.assertTrue(
         isinstance(robjects.default_ri2py(sexp), robjects.Environment))
Exemple #38
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 def testMapperR2Python_function(self):
     sexp = rinterface.globalenv.get("plot")
     ob = robjects.default_ri2py(sexp)
     self.assertTrue(isinstance(ob, robjects.Function))