added sphinx documentation

DylAFC.py

@@ -1,10 +1,11 @@
+#!/usr/bin/python3.6
+import os
+import socket
+import time
+import numpy as np
 from sys import argv
 from tkinter import *
 from PIL import ImageTk, Image
-import os
-import socket
-from numpy.random import random, randint
-from time import sleep, time
 class AFC:
 	"""A Class for doing AFC studies. This one only does 2AFC. It is used for integrating with a tkinter interface as seen in DylAFC."""
 	def __init__(self, posDir: str, negDir: str, ansDir: str, ip: str, port: str, n0: int, n1: int, logFile: str):
@@ -37,7 +38,7 @@ def connect(self):
 				s.connect((self.ip, int(self.port)))
 				break
 			except ConnectionRefusedError:
-				sleep(0.1)
+				time.sleep(0.1)
 		data: bytes = s.recv(10)
 		if data == b"I'm ready!":
 			s.send(b'\x02' + self.n0.to_bytes(4, 'little') + self.n1.to_bytes(4, 'little') + b'\x03')
@@ -103,14 +104,14 @@ def run(self):
 		if self.mode.get() == 'training':
 			if self.counter <= 0 and self.decision == -1: #put up new pictures
 				if self.ready:
-					if random() > 0.5:
-						self.imgID1: int = randint(0, self.n0 - 1)
-						self.imgID2: int = randint(self.n0, self.n1 + self.n0 - 1)
+					if np.random.random() > 0.5:
+						self.imgID1: int = np.random.randint(0, self.n0 - 1)
+						self.imgID2: int = np.random.randint(self.n0, self.n1 + self.n0 - 1)
 						self.showPics(self.imgID1, self.imgID2)
 						self.answer: str = 'right'
 					else:
-						self.imgID1: int = randint(self.n0, self.n1 + self.n0 - 1)
-						self.imgID2: int =  randint(0, self.n0 - 1)
+						self.imgID1: int = np.random.randint(self.n0, self.n1 + self.n0 - 1)
+						self.imgID2: int =  np.random.randint(0, self.n0 - 1)
 						self.showPics(self.imgID1, self.imgID2)
 						self.answer: str = 'left'
 					self.ready: bool = False
@@ -144,7 +145,7 @@ def run(self):
 							self.data: bytes = data
 							#print(img1, img2)
 							self.showPics(self.imgID1, self.imgID2)
-							self.t1: float = time()
+							self.t1: float = time.time()
 							root.update()
 							self.ready: bool = False
 				except ConnectionResetError:
@@ -161,7 +162,7 @@ def run(self):
 					payload: bytes = (0).to_bytes(4, 'little') + self.data[1:5]
 					des: int = self.imgID2
 				try:
-					self.f.write(f"{self.images[self.imgID1].filename} {self.images[self.imgID2].filename} {self.images[des].filename} {time() - self.t1}\n")
+					self.f.write(f"{self.images[self.imgID1].filename} {self.images[self.imgID2].filename} {self.images[des].filename} {time.time() - self.t1}\n")
 					self.s.send(b'\x02' + payload + b'\x03')
 				except ConnectionResetError:
 					print("Client Disconnected")

DylAnalyzer.py

@@ -1,13 +1,14 @@
+#!/usr/bin/python3.6
 import pickle
 import json
 import ROC1
 import tqdm
+import sys
+import os
 import numpy as np
 np.seterr(divide='ignore', invalid='ignore')
 import matplotlib.pyplot as plt
 from matplotlib.colors import LogNorm
-from os import stat
-from sys import getsizeof, argv
 from scipy import stats
 from multiprocessing import Pool
 from DylComp import Comparator
@@ -35,7 +36,7 @@ def analyzeMergeSims(fileName: str, length: int, layers: int, justOne: bool=Fals
 	varEstimates: np.ndarray = np.zeros((layers, 0))
 	aucs: np.ndarray = np.zeros((layers, 0))
 	iters: int = 0
-	fileLength: int = stat(fileName).st_size
+	fileLength: int = os.stat(fileName).st_size
 	old: int = 0
 	with open(fileName, "rb") as f, tqdm.tqdm(total=fileLength, unit="B", unit_scale=True, disable=not bar) as pBar:
 		# each simulation is one pickle, so need to depickle one at a time
@@ -78,7 +79,7 @@ def analyzeMergeSims(fileName: str, length: int, layers: int, justOne: bool=Fals
 
 				# update how many bytes were read
 				pBar.update(f.tell() - old)
-				pBar.desc: str = f"{iters}/{iterEstimate}, {reshapeCount}, {getsizeof(unpickler)}"
+				pBar.desc: str = f"{iters}/{iterEstimate}, {reshapeCount}, {sys.getsizeof(unpickler)}"
 				old: int = f.tell()
 
 				if justOne:
@@ -244,18 +245,20 @@ def analyzeReaderStudies(resultsFile, directory, n0):
 
 
 if __name__ == "__main__":
-	if len(argv) > 1 and (argv[1] == '2' or argv[1] == '1'):
-		if argv[1] == '2':
+	if len(sys.argv) > 1:
+		if sys.argv[1] == '2' and len(sys.argv) >= 4:
 			test: int = 2
-		elif argv[1] == '1':
+		elif sys.argv[1] == '1':
 			test: int = 1
+		else:
+			test: int = -1
 	else:
-		test = -1
+		test: int = -1
 	if test == 1:
 		# Shows the 5 plot dashboard for studies
 		length: int = 256
 		layers: int = 8
-		varEstimate, avgAUC, avgMSETrues, avgMSEEmpiric, avgComps, avgHanleyMNeil, avgEstimates, avgMinSeps, varAUCnp, stdVarEstimate, avgPC, iters = analyzeMergeSims(argv[2], length, layers, bar=True)
+		varEstimate, avgAUC, avgMSETrues, avgMSEEmpiric, avgComps, avgHanleyMNeil, avgEstimates, avgMinSeps, varAUCnp, stdVarEstimate, avgPC, iters = analyzeMergeSims(sys.argv[2], length, layers, bar=True)
 		labels: list = [f'{np.median(list(filter(lambda x: x != 0, avgMinSeps[0]))):3.02f}']
 		for val in np.median(avgMinSeps, axis=0)[1:]:
 			labels.append(f'{val:3.02f}')
@@ -336,9 +339,9 @@ def permutation(arr: list, D0: list, D1: list):
 		n0: int = 128
 		n1: int = 128
 
-		with open(argv[2]) as f:
+		with open(sys.argv[2]) as f:
 			results: dict = json.load(f)
-		with open(argv[3]) as f:
+		with open(sys.argv[3]) as f:
 			names: list = f.read().split()
 		if max((len(files) for files in results.values())) == 4:
 			fig, (scatterAxes, timeAxes, tauAxes) = plt.subplots(ncols=3, nrows=3)
@@ -439,11 +442,11 @@ def permutation(arr: list, D0: list, D1: list):
 
 			print(f"{reader} {np.mean(scaleTimes):0.3f}\t\t{np.std(scaleTimes):0.3f}\t\t{np.mean(mergeTimes):0.3f}\t\t\t{np.std(mergeTimes):0.3f}\t\t{tau:0.3f}\t{np.std(taus):0.3f}")
 		fig.set_size_inches(12, 8)
-		if len(argv) == 5:
-			plt.savefig(argv[4], bbox_inches = 'tight', pad_inches = 0)
+		if len(sys.argv) == 5:
+			plt.savefig(sys.argv[4], bbox_inches = 'tight', pad_inches = 0)
 		else:
 			plt.show()
 	else:
 		print("Usage:")
-		print(f"{__file__} [json results file] [optional output directory]")
-		print(f"{__file__} [simulation results file]")
+		print(f"{__file__} 1 [simulation results file]")
+		print(f"{__file__} 2 [json results file for reader studies] [names.txt filename] [optional output directory]")

DylComp.py

@@ -1,13 +1,12 @@
 #! /usr/bin/python3
+import pickle
 import numpy as np
 from scipy.stats import kendalltau
 from ROC1 import rocxy
 np.seterr(all="ignore")
 from warnings import filterwarnings
 filterwarnings("ignore")
 import socket
-from numpy.random import random
-from pickle import dump
 class Comparator:
 	"""A class for comparing 2 values.
 	Controlled with the optimizaiton level and if you want random decisions or not
@@ -310,7 +309,7 @@ def max(self, arr: list, tryingAgain=False) -> (int, int):
 				print(data, self.desHist)
 				raise ConnectionError("shoulda gotten that")
 			self.record(arr)
-		flipped: bool = random() > 0.5
+		flipped: bool = np.random.random() > 0.5
 		if flipped:
 			payload: bytes = b'\x02' + arr[1].to_bytes(4, 'little') + arr[0].to_bytes(4, 'little') + b'\x03'
 		else:
@@ -431,4 +430,4 @@ def max(self, arr: list, tryingAgain=False) -> (int, int):
 				plt.savefig("temp.svg")
 				replace("temp.svg", "figure.svg")
 		with open(argv[3], "wb") as f:
-			dump((avgROC, roc4), f)
+			pickle.dump((avgROC, roc4), f)

DylData.py

@@ -1,3 +1,4 @@
+#!/usr/bin/python3.6
 import numpy as np
 np.seterr(all="ignore")
 def continuousScale(*args):

DylMath.py

@@ -1,3 +1,4 @@
+#!/usr/bin/python3.6
 import ROC1
 import numpy as np
 np.set_printoptions(threshold=np.inf)

DylMerger.py

@@ -1,3 +1,4 @@
+#!/usr/bin/python3.6
 class MultiMerger:
 	def __init__(self, groups: list, comp, start=0, stop=0, toggle:bool=True):
 		groups: list = list(filter(lambda x: len(x) > 0, groups))

DylScale.py

@@ -1,11 +1,11 @@
 #! /usr/bin/python3
 import os
+from numpy import random
 from sys import argv
 from tkinter.constants import *
 from tkinter import *
 from PIL import ImageTk, Image, ImageDraw
 from time import time
-from numpy.random import shuffle
 class Rating:
 	"""A class for displaying an image and recording the ratins and timings of the reader.
 	Label parameter is the label where the image is going to be drawn.
@@ -33,7 +33,7 @@ def __init__(self, posDir: str, negDir: str, n: int, outputFile: str, offset: st
 		self.images: list = [ImageTk.PhotoImage(img) for img in self.images]
 		for i, image in enumerate(self.images):
 			setattr(image, "filename", names[i])
-		shuffle(self.images)
+		random.shuffle(self.images)
 		self.label = label
 		print()
 
@@ -159,7 +159,7 @@ def __init__(self, master, from_color, to_color, width=None, height=None, orient
 	ax2.plot(times)
 	ax2.set_title(f"Avg time {np.mean(times):0.2f}s")
 	plt.show()
-elif len(argv) < 5:
+elif len(argv) != 5 and len(argv) != 6:
 	print(f"Usage: \n\tpython3 {__file__} [signal present directory] [signal absent directory] [n] [output file] [offset (optional)]\n\tpython3 {__file__} [results file]")
 else:
 	IMGWIDTH: int = 600
@@ -171,21 +171,26 @@ def __init__(self, master, from_color, to_color, width=None, height=None, orient
 	label = Label(root)
 	if len(argv) < 6:
 		argv.append("0")
-	rating = Rating(*argv[1:], label)
-	label.configure(image=rating.images[0])
-	label.grid(row=1, column=0)
-	ticks = Frame(root)
-	ticks.grid(row=1, column=1)
-	for tickmark in range(0, 110, 10):
-		text = Label(ticks, text=str(tickmark))
-		row: int = 10-(tickmark//10)
-		text.grid(row=row, column=0, sticky=E, pady=18)
-	gradient = GradientFrame(root, from_color="#000000", to_color="#FFFFFF", height=IMGHEIGHT, width=100, orient=HORIZONTAL)
-	gradient.grid(row=1, column=2)
-	rating.canvas = gradient
-	gradient.bind("<Button-1>", rating.drawBar)
-	button = Button(text="next", command=rating.next)
-	button.grid(row=2, column=2)
-	root.bind("<Return>", rating.next)
-	rating.t1 = time()
-	root.mainloop()
+	try:
+		rating = Rating(*argv[1:], label)
+		label.configure(image=rating.images[0])
+		label.grid(row=1, column=0)
+		ticks = Frame(root)
+		ticks.grid(row=1, column=1)
+		for tickmark in range(0, 110, 10):
+			text = Label(ticks, text=str(tickmark))
+			row: int = 10-(tickmark//10)
+			text.grid(row=row, column=0, sticky=E, pady=18)
+		gradient = GradientFrame(root, from_color="#000000", to_color="#FFFFFF", height=IMGHEIGHT, width=100, orient=HORIZONTAL)
+		gradient.grid(row=1, column=2)
+		rating.canvas = gradient
+		gradient.bind("<Button-1>", rating.drawBar)
+		button = Button(text="next", command=rating.next)
+		button.grid(row=2, column=2)
+		root.bind("<Return>", rating.next)
+		rating.t1 = time()
+		root.mainloop()
+
+	except ValueError:
+		print("Invalid Arguments")
+		root.destroy()

DylSort.py

@@ -1,3 +1,4 @@
+#!/usr/bin/python3.6
 import numpy as np
 from sys import argv
 from DylMath import runStats, graphROCs
@@ -266,7 +267,6 @@ def treeMergeSort(arr: list, comp, statParams=None, n: int=2, combGroups: bool=T
 		length: int = int(2**power*(2/3))
 		power += 1
 		yStep: float = length / power
-		print(yStep)
 		fig, axes = plt.subplots(ncols=2, nrows=1)
 		for ax in axes:
 			if ax == axes[0]:

README.rst

@@ -193,7 +193,7 @@ Graphs and Where to Find Them
    ``python3 DylSort.py 5``
 -  Average ROC for each layer as a merge simulation progresses ->
    ``python3 DylSort.py 3 <overlapping (defualt True)>``
--  ROC curves for merge sort vs elo -> ``python3 Elo.py``
+-  ROC curves for merge sort vs elo -> ``python3 elo.py``
 
 .. |forthebadge made-with-python| image:: http://ForTheBadge.com/images/badges/made-with-python.svg
    :target: https://www.python.org/

docs/DylAnalyzer.html

@@ -19,12 +19,14 @@
 <tr><td bgcolor="#aa55cc"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
 <td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="ROC1.html">ROC1</a><br>
 <a href="json.html">json</a><br>
-</td><td width="25%" valign=top><a href="numpy.html">numpy</a><br>
+<a href="numpy.html">numpy</a><br>
+</td><td width="25%" valign=top><a href="os.html">os</a><br>
 <a href="pickle.html">pickle</a><br>
-</td><td width="25%" valign=top><a href="matplotlib.pyplot.html">matplotlib.pyplot</a><br>
-<a href="scipy.stats.html">scipy.stats</a><br>
-</td><td width="25%" valign=top><a href="tqdm.html">tqdm</a><br>
-</td></tr></table></td></tr></table><p>
+<a href="matplotlib.pyplot.html">matplotlib.pyplot</a><br>
+</td><td width="25%" valign=top><a href="scipy.stats.html">scipy.stats</a><br>
+<a href="sys.html">sys</a><br>
+<a href="tqdm.html">tqdm</a><br>
+</td><td width="25%" valign=top></td></tr></table></td></tr></table><p>
 <table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
 <tr bgcolor="#eeaa77">
 <td colspan=3 valign=bottom>&nbsp;<br>
@@ -42,36 +44,12 @@
  <dl><dt><a name="-analyzeScaleStudy"><strong>analyzeScaleStudy</strong></a>(fileName:str, names:list=None) -&gt; tuple</dt><dd><tt>Analyzes&nbsp;a&nbsp;scale&nbsp;study.<br>
 If&nbsp;names&nbsp;parameter&nbsp;given,&nbsp;filters&nbsp;for&nbsp;only&nbsp;those&nbsp;names.<br>
 Names&nbsp;can&nbsp;be&nbsp;any&nbsp;type&nbsp;of&nbsp;iterable.</tt></dd></dl>
- <dl><dt><a name="-getsizeof"><strong>getsizeof</strong></a>(...)</dt><dd><tt><a href="#-getsizeof">getsizeof</a>(object,&nbsp;default)&nbsp;-&gt;&nbsp;int<br>
-&nbsp;<br>
-Return&nbsp;the&nbsp;size&nbsp;of&nbsp;object&nbsp;in&nbsp;bytes.</tt></dd></dl>
- <dl><dt><a name="-stat"><strong>stat</strong></a>(path, *, dir_fd=None, follow_symlinks=True)</dt><dd><tt>Perform&nbsp;a&nbsp;stat&nbsp;system&nbsp;call&nbsp;on&nbsp;the&nbsp;given&nbsp;path.<br>
-&nbsp;<br>
-&nbsp;&nbsp;path<br>
-&nbsp;&nbsp;&nbsp;&nbsp;Path&nbsp;to&nbsp;be&nbsp;examined;&nbsp;can&nbsp;be&nbsp;string,&nbsp;bytes,&nbsp;a&nbsp;path-like&nbsp;object&nbsp;or<br>
-&nbsp;&nbsp;&nbsp;&nbsp;open-file-descriptor&nbsp;int.<br>
-&nbsp;&nbsp;dir_fd<br>
-&nbsp;&nbsp;&nbsp;&nbsp;If&nbsp;not&nbsp;None,&nbsp;it&nbsp;should&nbsp;be&nbsp;a&nbsp;file&nbsp;descriptor&nbsp;open&nbsp;to&nbsp;a&nbsp;directory,<br>
-&nbsp;&nbsp;&nbsp;&nbsp;and&nbsp;path&nbsp;should&nbsp;be&nbsp;a&nbsp;relative&nbsp;string;&nbsp;path&nbsp;will&nbsp;then&nbsp;be&nbsp;relative&nbsp;to<br>
-&nbsp;&nbsp;&nbsp;&nbsp;that&nbsp;directory.<br>
-&nbsp;&nbsp;follow_symlinks<br>
-&nbsp;&nbsp;&nbsp;&nbsp;If&nbsp;False,&nbsp;and&nbsp;the&nbsp;last&nbsp;element&nbsp;of&nbsp;the&nbsp;path&nbsp;is&nbsp;a&nbsp;symbolic&nbsp;link,<br>
-&nbsp;&nbsp;&nbsp;&nbsp;stat&nbsp;will&nbsp;examine&nbsp;the&nbsp;symbolic&nbsp;link&nbsp;itself&nbsp;instead&nbsp;of&nbsp;the&nbsp;file<br>
-&nbsp;&nbsp;&nbsp;&nbsp;the&nbsp;link&nbsp;points&nbsp;to.<br>
-&nbsp;<br>
-dir_fd&nbsp;and&nbsp;follow_symlinks&nbsp;may&nbsp;not&nbsp;be&nbsp;implemented<br>
-&nbsp;&nbsp;on&nbsp;your&nbsp;platform.&nbsp;&nbsp;If&nbsp;they&nbsp;are&nbsp;unavailable,&nbsp;using&nbsp;them&nbsp;will&nbsp;raise&nbsp;a<br>
-&nbsp;&nbsp;NotImplementedError.<br>
-&nbsp;<br>
-It's&nbsp;an&nbsp;error&nbsp;to&nbsp;use&nbsp;dir_fd&nbsp;or&nbsp;follow_symlinks&nbsp;when&nbsp;specifying&nbsp;path&nbsp;as<br>
-&nbsp;&nbsp;an&nbsp;open&nbsp;file&nbsp;descriptor.</tt></dd></dl>
 </td></tr></table><p>
 <table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
 <tr bgcolor="#55aa55">
 <td colspan=3 valign=bottom>&nbsp;<br>
 <font color="#ffffff" face="helvetica, arial"><big><strong>Data</strong></big></font></td></tr>
 
 <tr><td bgcolor="#55aa55"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
-<td width="100%"><strong>__annotations__</strong> = {}<br>
-<strong>argv</strong> = ['/usr/lib/python3.6/pydoc.py', '-w', './']</td></tr></table>
+<td width="100%"><strong>__annotations__</strong> = {}</td></tr></table>
 </body></html>