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[change] extracted plotting and started new module for plotting; improved docstring quality

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This commit is contained in:
Sebastian Wehling-Benatelli 2016-08-18 10:22:30 +02:00
parent 7921d12c80
commit 71f59b3c64
3 changed files with 132 additions and 109 deletions
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157
pylot/core/pick/compare.py
View File

@ -2,6 +2,7 @@
# -*- coding: utf-8 -*-
import copy
import operator
import os
import numpy as np
import glob
@ -151,7 +152,6 @@ class Comparison(object):
return rlist
def get_array(self, phase, method_name):
import operator
method = operator.methodcaller(method_name)
pdf_list = self.get_all(phase)
rarray = map(method, pdf_list)
@ -258,6 +258,15 @@ class PDFDictionary(object):
'time is not implemented yet! Sorry!')
return PDFDictionary(picksdict_from_picks(cat[0]))
def get_all(self, phase):
rlist = list()
for phases in self.pdf_data.values():
try:
rlist.append(phases[phase])
except KeyError:
continue
return rlist
def generate_pdf_data(self, type='exp'):
"""
Returns probabiliy density function dictionary containing the
@ -350,31 +359,9 @@ class PDFstatistics(object):
self.directory = directory
self.evtlist = list()
self.return_phase = None
self.make_fnlist()
def readTheta(self, arname, dir, fnpattern):
"""
Loads an array from file into object instance.
:param arname: Name of Array beeing created.
:type arname: string
:param dir: Directory where file is to be found.
:type dir: string
:param fnpattern: file name pattern for reading multiple files into one array.
:type fnpattern: string
:return: a list with all args* from the files.
"""
exec('self.' + arname +' = []')
filelist = glob.glob1(dir, fnpattern)
for file in filelist:
fid = open(os.path.join(dir,file), 'r')
list = []
for line in fid.readlines():
list.append(eval(line))
exec('self.' + arname + ' += list')
fid.close()
def makeFileList(self, fn_pattern='*.xml'):
def make_fnlist(self, fn_pattern='*.xml'):
"""
Takes a file pattern and searches for that recursively in the set path for the object.
:param fn_pattern: A pattern that can identify all datafiles. Default Value = '*.xml'
@ -389,7 +376,6 @@ class PDFstatistics(object):
evtlist.append(os.path.join(root, file))
self.evtlist = evtlist
def __iter__(self):
"""Iterating over the PDFstatistics object yields every single pdf from the list of events"""
assert isinstance(self.return_phase, str), 'phase has to be set before being able to iterate over items...'
@ -401,7 +387,6 @@ class PDFstatistics(object):
except KeyError:
continue
def set_return_phase(self, type):
"""
Sets the phase typ of event data that is returned on iteration over the object.
@ -414,40 +399,45 @@ class PDFstatistics(object):
else:
self.return_phase = type.upper()
def getQD(self,value):
def quantile_distances(self, value):
"""
Takes a probability value and and returns the distance
between two complementary quantiles.
For example: getQD(0.3) yields Quantile(1-0.3) - Quantile(0.3)
:param value: 0 < value < 0.5
takes a probability value and and returns the distance
between two complementary quantiles
.. math::
QA_\alpha = Q(1 - \alpha) - Q(\alpha)
:param value: probability value :math:\alpha
:type value: float
:return: returns a list of all quantile distances for all pdfs in
:return: list of all quantile distances for all pdfs in
the list of events.
"""
QDlist = []
rlist = []
for pdf in self:
QD = pdf.quantile_distance(value)
QDlist.append(QD)
return QDlist
rval = pdf.quantile_distance(value)
rlist.append(rval)
return rlist
def getQDQ(self,value):
def quantile_distance_fractions(self, value):
"""
Takes a probability value and and returns the fraction of
two quantile distances.
For example:
getQDQ(x) = getQD(0.5-x)/getQD(x)
(Quantile(1-0.5-x) - Quantile(x)) / (Quantile(1-x) - Quantile(x))
:param value: 0 < value < 0.25
takes a probability value and returns the fraction of two
corresponding quantile distances
.. math::
Q\Theta_\alpha = \frac{QA(0.5 - \alpha)}{QA(\alpha)}
:param value: probability value :math:\alpha
:return: returns a list of all quantile fractions for all pdfs in
the list of events.
"""
QDQlist = []
rlist = list()
for pdf in self:
QDQ = pdf.qtile_dist_quot(value)
QDQlist.append(QDQ)
return QDQlist
rval = pdf.quantile_dist_frac(value)
rlist.append(rval)
return rlist
def getSTD(self):
@ -481,61 +471,6 @@ class PDFstatistics(object):
'Actual phase type: {0}'.format(self.return_phase))
def getBinList(self,l_boundary,u_boundary,nbins = 100):
"""
Helper function for self.histplot(). Takes in two boundaries and
a number of bins and creates a list of bins which can be passed
to self.histplot().
:param l_boundary: Any number.
:type l_boundary: float
:param u_boundary: Any number that is greater than l_boundary.
:type u_boundary: float
:param nbins: Any positive integer.
:type nbins: int
:return: A list of equidistant bins.
"""
if u_boundary <= l_boundary:
raise ValueError('Upper boundary must be greather than lower!')
elif nbins <= 0:
raise ValueError('Number of bins is not valid.')
binlist = []
for i in range(nbins):
binlist.append(l_boundary + i*(u_boundary-l_boundary)/nbins)
return binlist
def histplot(self, array, binlist, xlab = 'Values',
ylab = 'Frequency', title = None, fnout = None):
"""
Method to quickly show some distribution of data. Takes array like data,
and a list of bins. Editing detail and inserting a legend is not possible.
:param array: List of values.
:type array: Array like
:param binlist: List of bins.
:type binlist: list
:param xlab: A label for the x-axes.
:type xlab: str
:param ylab: A label for the y-axes.
:type ylab: str
:param title: A title for the Plot.
:type title: str
:param fnout: A path to save the plot instead of showing.
Has to contain filename and type. Like: 'path/to/file.png'
:type fnout. str
:return: -
"""
import matplotlib.pyplot as plt
plt.hist(array,bins = binlist)
plt.xlabel(xlab)
plt.ylabel(ylab)
if title:
plt.title(title)
if fnout:
plt.savefig(fnout)
else:
plt.show()
def getPDFDict(self, month, evt):
"""
Helper function for __iter__(). Should not be called directly.
@ -583,13 +518,19 @@ class PDFstatistics(object):
def main():
root_dir ='/home/sebastianp/Codetesting/xmls/'
Insheim = PDFstatistics(root_dir)
Insheim.makeFileList()
Insheim.make_fnlist()
Insheim.set_return_phase('p')
Insheim.getSTD()
qdlist = Insheim.getQDQ(0.3)
binlist = Insheim.getBinList(0.,3.)
qdlist = Insheim.quantile_distance_fractions(0.2)
print qdlist
if __name__ == "__main__":
main()
import cProfile
pr = cProfile.Profile()
pr.enable()
main()
pr.disable()
# after your program ends
pr.print_stats(sort="calls")

27
pylot/core/util/pdf.py
View File

@ -363,6 +363,18 @@ class ProbabilityDensityFunction(object):
return m
def quantile_distance(self, prob_value):
"""
takes a probability value and and returns the distance
between two complementary quantiles
.. math::
QA_\alpha = Q(1 - \alpha) - Q(\alpha)
:param value: probability value :math:\alpha
:type value: float
:return: quantile distance
"""
if 0 >= prob_value or prob_value >= 0.5:
raise ValueError('Value out of range.')
ql = self.quantile(prob_value)
@ -370,7 +382,20 @@ class ProbabilityDensityFunction(object):
return qu - ql
def qtile_dist_quot(self,x):
def quantile_dist_frac(self, x):
"""
takes a probability value and returns the fraction of two
corresponding quantile distances (
:func:`pylot.core.util.pdf.ProbabilityDensityFunction
#quantile_distance`)
.. math::
Q\Theta_\alpha = \frac{QA(0.5 - \alpha)}{QA(\alpha)}
:param value: probability value :math:\alpha
:return: quantile distance fraction
"""
if x <= 0 or x >= 0.25:
raise ValueError('Value out of range.')
return self.quantile_distance(0.5-x)/self.quantile_distance(x)

57
pylot/core/util/plotting.py Normal file
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@ -0,0 +1,57 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import matplotlib.pyplot as plt
def create_bin_list(l_boundary, u_boundary, nbins=100):
"""
takes two boundaries and a number of bins and creates a list of bins for
histogram plotting
:param l_boundary: Any number.
:type l_boundary: float
:param u_boundary: Any number that is greater than l_boundary.
:type u_boundary: float
:param nbins: Any positive integer.
:type nbins: int
:return: A list of equidistant bins.
"""
if u_boundary <= l_boundary:
raise ValueError('Upper boundary must be greather than lower!')
elif nbins <= 0:
raise ValueError('Number of bins is not valid.')
binlist = []
for i in range(nbins):
binlist.append(l_boundary + i * (u_boundary - l_boundary) / nbins)
return binlist
def histplot(array, binlist, xlab='Values',
ylab='Frequency', title=None, fnout=None):
"""
function to quickly show some distribution of data. Takes array like data,
and a list of bins. Editing detail and inserting a legend is not possible.
:param array: List of values.
:type array: Array like
:param binlist: List of bins.
:type binlist: list
:param xlab: A label for the x-axes.
:type xlab: str
:param ylab: A label for the y-axes.
:type ylab: str
:param title: A title for the Plot.
:type title: str
:param fnout: A path to save the plot instead of showing.
Has to contain filename and type. Like: 'path/to/file.png'
:type fnout. str
:return: -
"""
plt.hist(array, bins=binlist)
plt.xlabel(xlab)
plt.ylabel(ylab)
if title:
plt.title(title)
if fnout:
plt.savefig(fnout)
else:
plt.show()