marcel/pylot
3
0
Fork 0
Code Issues 17 Pull Requests 1 Releases Wiki Activity

[documentation] adding docstring to all the methods.

Browse Source
This commit is contained in:
sebastianp 2016-08-11 16:13:53 +02:00
parent c72ed1e169
commit 36e7bc1bb2
3 changed files with 137 additions and 21 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

146
pylot/core/pick/compare.py
View File

@ -339,16 +339,30 @@ class PDFDictionary(object):
class PDFstatistics(object):
'''
To do:
plots for std, quantiles,
'''
"""
This object can be used to get various statistic values from probabillity density functions.
Takes a path as argument.
"""
def __init__(self, directory):
"""Initiates some values needed when dealing with pdfs later"""
self.directory = directory
self.evtlist = list()
self.return_phase = None
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:
@ -359,8 +373,14 @@ class PDFstatistics(object):
exec('self.' + arname + ' += list')
fid.close()
def makeFileList(self, fn_pattern='*.xml'):
evtlist = list()
"""
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'
:type fn_pattern: string
:return: creates a list of events saved in the PDFstatistics object.
"""
evtlist = glob.glob1((os.path.join(self.directory)), fn_pattern)
if not evtlist:
for root, _, files in os.walk(self.directory):
@ -369,7 +389,9 @@ 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...'
for evt in self.evtlist:
self.getPDFDict(self.directory, evt)
@ -379,13 +401,30 @@ 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.
:param type: can be either p (p-phase) or s (s-phase).
:type type: string
:return: -
"""
if type.upper() not in 'PS':
raise ValueError("phase type must be either 'P' or 'S'!")
else:
self.return_phase = type.upper()
def getQD(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
:type value: float
:return: returns a list of all quantile distances for all pdfs in
the list of events.
"""
QDlist = []
for pdf in self:
QD = pdf.quantile_distance(value)
@ -394,6 +433,16 @@ class PDFstatistics(object):
def getQDQ(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
:return: returns a list of all quantile fractions for all pdfs in
the list of events.
"""
QDQlist = []
for pdf in self:
QDQ = pdf.qtile_dist_quot(value)
@ -402,6 +451,12 @@ class PDFstatistics(object):
def getSTD(self):
"""
Iterates over PDFstatistics object and returns the standard
deviation of all pdfs in the list of events.
:return: saves an instance of self.p_stdarray or
self.s_stdarray, depending on set phase.
"""
std = []
for pdf in self:
try:
@ -413,6 +468,10 @@ class PDFstatistics(object):
def set_stdarray(self, array):
"""
Helper function for self.getSTD(). This function
should not be called directly.
"""
if self.return_phase == 'P':
self.p_stdarray = array
elif self.return_phase == 'S':
@ -423,6 +482,22 @@ class PDFstatistics(object):
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)
@ -430,28 +505,57 @@ class PDFstatistics(object):
def histplot(self, array, binlist, xlab = 'Values',
ylab = 'Frequency', title = None, label=None,
fnout = None):
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('Values')
plt.ylabel('Frequency')
plt.xlabel(xlab)
plt.ylabel(ylab)
if title:
title_str = 'Quantile distance quotient distribution'
if label:
title_str += ' (' + label + ')'
plt.title(title_str)
plt.title(title)
if fnout:
plt.savefig(fnout+'histplot.png')
plt.savefig(fnout)
else:
plt.show()
def getPDFDict(self, month, evt):
"""
Helper function for __iter__(). Should not be called directly.
"""
self.pdfdict = PDFDictionary.from_quakeml(os.path.join(self.directory,month,evt))
def getStatistics(self):
"""
On call function will get mean, median and standard deviation values
from self.p_stdarray and self.s_stdarray. Both must be
instances before calling this function.
:return: Creates instances of self.p_mean, self.p_std_std and self.p_median
for both phases (simultaneously) for the PDFstatistics object.
"""
if not self.p_stdarray or not self.s_stdarray:
raise NotImplementedError('Arrays are not properly set yet!')
elif type(self.p_stdarray) != type(np.zeros(1)) or type(self.s_stdarray) != type(np.zeros(1)):
raise TypeError('Array is not a proper numpy array.')
self.p_mean = self.p_stdarray.mean()
self.p_std_std = self.p_stdarray.std()
self.p_median = np.median(self.p_stdarray)
@ -460,12 +564,22 @@ class PDFstatistics(object):
self.s_median = np.median(self.s_stdarray)
def writeThetaToFile(self,array,out_dir,filename = None):
fid = open(os.path.join(out_dir,filename), 'w')
def writeThetaToFile(self,array,out_dir):
"""
Method to write array like data to file. Useful since acquiring can take
serious amount of time when dealing with large databases.
:param array: List of values.
:type array: list
:param out_dir: Path to save file to including file name.
:type out_dir: str
:return: Saves a file at given output directory.
"""
fid = open(os.path.join(out_dir), 'w')
for val in array:
fid.write(str(val)+'\n')
fid.close()
def main():
root_dir ='/home/sebastianp/Codetesting/xmls/'
Insheim = PDFstatistics(root_dir)

4
pylot/core/util/pdf.py
View File

@ -363,13 +363,15 @@ class ProbabilityDensityFunction(object):
return m
def quantile_distance(self, prob_value):
if 0 >= prob_value or prob_value >= 0.5:
raise ValueError('Value out of range.')
ql = self.quantile(prob_value)
qu = self.quantile(1 - prob_value)
return qu - ql
def qtile_dist_quot(self,x):
if x <= 0 or x >= 0.5:
if x <= 0 or x >= 0.25:
raise ValueError('Value out of range.')
return self.quantile_distance(0.5-x)/self.quantile_distance(x)

8
pylot/core/util/utils.py
View File

@ -223,10 +223,10 @@ def getPatternLine(fn, pattern):
def isSorted(iterable):
'''
:param iterable:
:type iterable:
:return:
Takes an iterable and checks if args* are in order.
:param iterable: any with defined __ls__() and __gs__()
:type iterable: list
:return: Boolean
'''
return sorted(iterable) == iterable