def __init__(self, fileName):
#--------read and count chains and number of sites-------------
linesInBlock = 0
prevLineIsEmpty = False
emptyLine = "\n"
blockNum = 0
lineNum = 0
self.N = []
self.chain = []
self.chain.append(Chain.Chain())
with open(fileName) as fp:
for line in fp:
if (line == emptyLine):
if (prevLineIsEmpty == False):
self.N.append(lineNum)
blockNum = blockNum + 1
self.chain.append(Chain.Chain())
lineNum = 0
prevLineIsEmpty = True
else:
x, y, z = line.split()
self.chain[blockNum].pushCoordinates(
float(x), float(y), float(z))
lineNum = lineNum + 1
prevLineIsEmpty = False
#self.numBlocks = blockNum-1;
self.numBlocks = blockNum
#---------------------------end--------------------------------
print('Number of chains: %i.' % self.numBlocks)
def boundary(self, chain_or_cell):
"""
Return the boundary of the given chain or cell
"""
if isinstance(chain_or_cell, CubicalCell):
result = chain_or_cell.boundary(self.ring())
else:
result = sum([
chain_or_cell[cell] * cell.boundary(self.ring())
for cell in chain_or_cell
], Chain(self.dimension(), self.ring()))
# Project out cells not in complex
return sum([
result[cell] * ElementaryChain(cell, self.ring())
for cell in result if cell in self.cells()
], Chain(self.dimension(), self.ring()))
def project(self, chain):
"""
Project away all cells except critical cells
"""
return sum((chain[cell] * ElementaryChain(cell, self.ring())
for cell in chain if cell in self.cells()),
Chain(chain.dimension(), self.ring()))
def __init__(self):
super().__init__()
# genesis block
self.node_ = Node.Node("0", "127.0.0.1:10000", Chain.Chain())
self.node_.chain_.AddBlock(0)
self.uid_ = str(uuid4())
BCNet.nodes_[self.uid_] = self.node_
def reset_chain(self):
"""
Resets the Markov Chain which the sampler has constructed
"""
self.chain = Chain.Chain(self.initial_params)
self.current_params = self.initial_params
def sfmChainRestoreRender(chainFilePath):
# load the sfm chain
headStages, tailStages = Chain.StageRegistry.Load(chainFilePath)
# render the tail stage (pmvs)
print Chain.Render(tailStages[0], "persistence.txt")
def keymatchChains(imagePath):
# KeyMatchFull, KeyMatchGPU
imageSource = Sources.ImageSource(imagePath, "pgm")
sift = FeatureExtraction.Sift(imageSource, False, "SiftHess")
keyMatch = FeatureMatch.KeyMatch(sift, True, "KeyMatchFull", forceRun=True)
print Chain.Render(keyMatch,"UnitTest-keymatchChains-KeyMatchFull-log.txt")
def project(self, chain):
"""
Return the projection of a chain in the supercomplex
into the current complex. (i.e. drop cells not in self.cells())
"""
return sum((chain[cell] * ElementaryChain(cell, self.ring())
for cell in chain if cell in self.cells()),
Chain(chain.dimension(), self.ring()))
def newChain(self): """ creates and returns a new chain """ mychain = Chain() self.addChain(mychain) return mychain
def __init__(self, config, repnum):
"""Initialize the Replica() object."""
temp = config.REPLICATEMPS[repnum]
self.repnum = repnum
self.repname = 'rep' + string.zfill(str(repnum), 2)
self.repdir = config.DATADIR + self.repname
self.chain = Chain.Chain(config)
self.mc = Monty.Monty(config, temp, self.chain)
def homotopy(chain):
"""
Implement the discrete Morse homotopy gamma
"""
# We clone the input chain to prevent unexpected alterations
work_chain = copy.deepcopy(chain)
# We create a dictionary "priority" which gives the rank of queens.
# Lower priority numbers will be processed first (i.e. priority ranking, not priority value)
Queens = [Q for Q in cellcomplex if isQueen(Q)]
def AdjacentQueens(Q):
return [q for q in bd(M(Q)) if isQueen(q) and q != Q]
priority = {
Q: rank
for (rank, Q) in enumerate(TopologicalSort(Queens, AdjacentQueens))
}
# We arrange the priority queue for queens.
# We use an auxiliary set "enqueued" to prevent the same queen from being
# placed in the priority queue twice.
work_queue = PriorityQueue()
enqueued = set()
def enqueue(list_of_queens):
for Q in list_of_queens:
if Q in enqueued: continue
enqueued.add(Q)
work_queue.put((-priority[Q], Q))
# Initialize queue with the queens in the original chain
enqueue([Q for Q in work_chain if isQueen(Q)])
# Make a zero chain of correct dimension to store result in
gamma_chain = Chain(dim(chain) + 1, cellcomplex.ring())
# We iteratively process the maximal queen in "work_chain", each time
# adding the appropriate multiple of the boundary of its mating king in
# order to cancel it. Doing this can add new queens, which we enqueue.
# A theorem prevents previously processed queens from being "new_queens"
# We keep track of the king chain as we go.
while not work_queue.empty():
(rank, Q) = work_queue.get()
a = work_chain[Q]
if a == 0: continue
K = M(Q)
bd_K = bd(K)
b = bd_K[Q]
c = -a / b
gamma_chain[K] += c
work_chain += c * bd_K
enqueue([q for q in bd_K if isQueen(q) and q != Q])
return gamma_chain
def siftChains(imagePath):
#SiftWin32, SiftHess, SiftGPU, VLFeat
imageSource = Sources.ImageSource(imagePath, "pgm")
sift = FeatureExtraction.Sift(imageSource, False, "SiftWin32", forceRun=True)
# SiftWin32 only on windows
if (Common.Utility.OSName=="Windows"):
print Chain.Render(sift,"UnitTest-siftChains-SiftWin32-log.txt")
sift.SetProperty("Sift Method", "VLFeat")
print Chain.Render(sift,"UnitTest-siftChains-VLFeat-log.txt")
# daisy only on windows (note: this should not be the last test, as the descriptors are for ROIs)
if (Common.Utility.OSName=="Windows"):
imageSource = Sources.ImageSource(imagePath, "jpg")
daisy = FeatureExtraction.Daisy(imageSource, False, roi="0,0,50,50", forceRun=True)
print Chain.Render(daisy,"UnitTest-siftChains-daisy-log.txt")
sift.SetProperty("Sift Method", "SiftHess")
print Chain.Render(sift,"UnitTest-siftChains-SiftHess-log.txt")
def StartGame():
global objects
global pairs
global wind
global forces
global RUNNING
global PAUSED
global ONETIME
global TEST
objects=[]
forces = []
rad=const.SPHERE_RADIUS
#objects.append(Circle(rad, color=const.DARK_GRAY, width= 0, pos=[400,100], velo=[0,0], mass=math.inf))
firstBall=Circle(rad, color=const.DARK_GRAY, width= 0, pos=[400,100], velo=[0,0], mass=math.inf)
objects.append(Circle(rad, color=const.ORANGE, width=0, pos=[400,200], velo=[0,0], mass=const.REALISTIC_MASS))
objects.append(Circle(rad, color=const.YELLOW, width= 0, pos=[400,300], velo=[0,0], mass=const.REALISTIC_MASS))
objects.append(Circle(rad, color=const.GREEN, width= 0, pos=[400,400], velo=[0,0], mass=const.REALISTIC_MASS))
objects.append(Circle(rad, color=const.PINK, width= 0, pos=[400,500], velo=[0,0], mass=const.REALISTIC_MASS))
forces.append(Gravity(objects=objects.copy(), acc = [0, 9.8* const.MM_TO_PX]))
wind = AirDrag(windVel=[0,0], objects=objects.copy())
forces.append(wind)
pairs =[]
firstPair=[firstBall,objects[0]]
pairs.append(firstPair)
for i in range(len(objects)):
if(i < len(objects)-1):
obj1= objects[i]
obj2= objects[i+1]
pairs.append([obj1, obj2])
forces.append(Chain(k=const.SPRING_FORCE, naturalLen=const.NATURAL_LENGTH, damp=const.DAMPENING, pair=pairs))
#Add our Infinite mass circle after Forces:
objects.append(firstBall)
forces.append(Repulsion(k=const.SPRING_FORCE, objList=objects.copy(), pair=pairs))
RUNNING=True;
PAUSED=False;
GAMEOVER=False;
READ_FOR_PLAY_AGAIN=False;
startTime= time.time()
def renderChain2(self):
self.statusBox.clear()
if (not self.__visualizationsInitialized):
# get all tail stages, build "force run" map
tails = []
forceRuns = {}
for stage in Chain.StageRegistry.registry.GetStageInstances():
if (len(stage.GetOutputStages()) == 0): tails.append(stage)
if ("Force Run" in stage.GetPropertyMap().keys()):
forceRuns[stage] = stage.GetProperty("Force Run")
try:
# render once with the chain state as the user defined it
Chain.Render(tails)
except:
pass
finally:
# set all force runs to False as image views are initialized
for stage in forceRuns.keys():
stage.SetProperty("Force Run", False)
self.initializeVisualizations()
self.__visualizationsInitialized = True
for vis in self.__visualizations:
try:
vis.refresh()
except:
pass
# revert force runs
for stage, fr in forceRuns.iteritems():
stage.SetProperty("Force Run", fr)
else:
#for stage in self.__stages: stage.Reset()
for vis in self.__visualizations:
try:
vis.refresh()
except:
pass
def boundary(self, ring=int):
"""
Return boundary of elementary chain
in a hypothetical full complex
"""
# d((x,y)) = (dx, y) + (-1)**(dim(x)) (x,dy)
result = Chain(self.D - 1, ring)
sign = 1
for d, interval in enumerate(self.bounds()):
if interval[0] == interval[1]: continue
left = list(self.bounds())
right = list(self.bounds())
left[d] = (interval[0], interval[0])
right[d] = (interval[1], interval[1])
result[CubicalCell(left)] = ring(-sign)
result[CubicalCell(right)] = ring(sign)
sign = sign * -1
return result
def bundlerChain(imagePath):
# PMVS path
pmvsPath = os.path.join(imagePath,"pmvs")
# build chain
imageSource = Sources.ImageSource(imagePath, "jpg")
sift = FeatureExtraction.Sift(imageSource, False, "SiftHess")
keyMatch = FeatureMatch.KeyMatch(sift, False, "KeyMatchFull")
bundler = BundleAdjustment.Bundler([keyMatch, imageSource], forceRun=True)
radialUndistort = Cluster.RadialUndistort([bundler, imageSource], forceRun=True)
prepCmvsPmvs = Cluster.PrepCmvsPmvs(radialUndistort, pmvsPath, forceRun=True)
# cmvs not build on 32bit Linux yet
if (Common.Utility.PlatformName != "Linux32bit"):
cmvs = Cluster.CMVS(prepCmvsPmvs, forceRun=True)
pmvs = Cluster.PMVS(cmvs, forceRun=True)
else:
pmvs = Cluster.PMVS(prepCmvsPmvs, forceRun=True)
# render chain
print Chain.Render(pmvs,"UnitTest-bundlerChain-log.txt")
def generate(self, genAmount):
reddit = Reddit(client_id=Client_id, client_secret=Client_secret, password=Password,
user_agent=User_agent, username=Username)
reddit.read_only = True # makes the program like 2x faster
sub = reddit.subreddit(self.subreddit)
posts = sub.top(limit = self.numPosts)
chain = Chain()
for post in posts:
if not post.stickied and not post.title in self.filteredPosts and not 'battleforthenet' in post.url:
# print(post.title)
if not self.useCommentData:
post = toLetters(post.title)
chain.add_words(post)
continue
comments = post.comments
for i, comment in enumerate(comments):
if i>=6: break
comment = comment.body.replace('\n', ' ')
if self.lettersAndNumsOnly:
comment = toLetters(comment)
if not 'https' in comment:
# print(30*'-')
# print(comment)
chain.add_words(comment)
filename = 'r_' + self.subreddit + '.xml'
output = open(filename, 'w+')
if self.useCommentData:
output.write('r_'+self.subreddit)
else:
output.write('T r_' + self.subreddit)
# print(30*'=')
for x in range(genAmount):
output.write('\n'+chain.gen_messge())
def renderChain(self):
self.statusBox.clear()
tails = []
for stage in Chain.StageRegistry.registry.GetStageInstances():
if (len(stage.GetOutputStages()) == 0): tails.append(stage)
try:
Chain.Render(tails)
except:
pass
if (not self.__visualizationsInitialized):
self.initializeVisualizations()
self.__visualizationsInitialized = True
for vis in self.__visualizations:
try:
vis.refresh()
except:
pass
for pe in self.__propertyEditors.values():
pe.SetProperties()
self._properties["Prefix Name"] = prefixName
def GetOutputImagePath(self, inputImagePath):
# construct the output image path, including the prefix name
return os.path.join(self._properties["Output Image Path"],
self._properties["Prefix Name"] +
os.path.splitext(os.path.basename(inputImagePath))[0] +
"."+self._properties["Image Extension"])
def ProcessImage(self, inputImagePath, outputImagePath):
# copy the input to output
shutil.copy(inputImagePath, outputImagePath)
#################################################################################
# input/output image path
imagePath = os.path.abspath("../Datasets/ET")
imagePathOut = os.path.join(imagePath, "test")
Common.Utility.MakeDir(imagePathOut)
imageSource = Sources.ImageSource(imagePath, "jpg")
imageCopy = CopyImages(imageSource, "test-", imagePathOut, "jpg")
print Chain.Render(imageCopy)
def __init__(self,
initial_condition,
param_priors,
step_sigmas,
systematic_error=False,
degeneracy=True):
"""
sampler class
Parameters:
----------
initial_condition: Dictionary{String: float}
A dictionary defining the starting parameter values of the sampler
param_priors: Dictionary{String: String}
A dictionary defining the prior distributions of the input parameters
step_sigma: [floats]
A list containing the parameter step standard deviations. The parameter
standard deviations determine how far each step of the generating function
is allowed to attempt to travel
systematic_error: Boolean
Tells the sampler whether to calculate the likelihood
with or without using the systematic error
degeneracy: Boolean
Tells the sampler whether the degenerate relationship between
M and H0 should be preserved or discarded.
Attributes:
----------
chain: Chain
An instance of the Chain class which contains the
Markov Chain which the sampler is creating
LK: likelihood
An instance of the likelihood class which will
return the log-likelihood of each set of parameter
values
sys_error: boolean
The storage of the systematic_error input
initial_params: Dictionary{String: float}
The dictionary mapping the starting parameter values
to the parameters in question. Stored for the purpose
of calculating prior probability densities.
current_params: Dictionary{String: float}
The dictionary mapping the current parameter
values to the parameters in question
current_prior_p: float
The combined prior probability of the current parameter values
candidate_params: Dictionary{string: float}
The dictionary mapping the candidate parameter
values to the parameters in question.
candidate_prior_p: float
The combined prior probability of the candidate parameter values
param_priors: Dictionary{String: float}
The dictionary mapping each parameter to a
prior distribution. The float is assumed to
be the std of a gaussian distribution. If the value
is zero, then it is instead a uniform distribution
step_sigmas: [floats]
Storing the input step_sigmas as described above
cov_alpha: float
Determines the coefficient alpha multiplying the covariance
matrix
cov: array[floats]
The covariance matrix of the generating function
cov_inverse: array[floats]
The inverse of the covariance matrix
degeneracy: Boolean
Described above
Usage example:
---------------
import MCsampler
cov = np.identity()
initial_params = {"Omega_m": 0.3,
"Omega_lambda": 0.7,
"H0": 74.0,
"M_nuisance": -19.23,
"Omega_k": 0.0,
}
priors = {"Omega_m": 0.0,
"Omega_lambda": 0.0,
"H0": 0.0,
"M_nuisance": 0.042,
"Omega_k": 0.0
}
scaling = [0.1, 0.1, 1.0, 0.1, 0.1]
mcmc = MCsampler.MCMC(initial_params, priors, scaling, True, False)
mcmc.learncov(cov)
for _ in range(number_steps):
mcmc.add_to_chain()
chain = mcmc.return_chain()
"""
self.chain = Chain.Chain(initial_condition)
self.LK = likelihood.LK()
self.sys_error = systematic_error
self.initial_params = initial_condition
self.current_params = initial_condition
self.current_prior_p = 1.0
self.candidate_params = {}
self.candidate_prior_p = 1.0
self.param_priors = param_priors
self.step_sigmas = step_sigmas
self.cov_alpha = 0.1
self.cov = self.cov_alpha * np.identity(5)
self.cov_inverse = np.linalg.inv(self.cov)
self.degeneracy = degeneracy
# Copyright (c) 2012, Adam J. Rossi. All rights reserved. See README for licensing details.
import sys, os
sys.path.append(os.path.abspath("."))
import Chain # Chain must be imported first, requirement of registry
import Sources, FeatureExtraction, Common
# path to images
imagePath = os.path.abspath("../Datasets/ET")
# build chain
imageSource = Sources.ImageSource(imagePath, "jpg")
# insert tap point stage with print function
tap = Common.TapPoint(
imageSource, {Common.sfmImages: lambda x: "Image Path: " + x.GetPath()})
# insert tap point stage without print function
tap = Common.TapPoint(tap)
sift = FeatureExtraction.Sift(tap, False, "SiftHess")
# render chain
print Chain.Render(sift, "tapPoint.txt")
import Block
import Chain
if __name__ == "__main__":
blockchain = Chain.Chain()
print("Starting the Program")
print(blockchain.chain)
blockchain.get_data(
sender="0",
receiver="Jacob",
amount=1
)
block = blockchain.mine_block("Miner")
block = blockchain.mine_block("Andrew")
print("Mining Sucuessful")
print(blockchain.chain)
print("\n\n")
for block in blockchain.chain:
block.print()
print("")
# Copyright (c) 2014, Adam J. Rossi. All rights reserved. See README for licensing details.
import sys, os
sys.path.append(os.path.abspath("."))
import Chain
import Sources, OpenCV
imagePath = os.path.abspath("../Datasets/ET")
imageSource = Sources.ImageSource(imagePath, "jpg")
fd = OpenCV.FeatureDetector(imageSource, forceRun=True)
fm = OpenCV.FeatureMatcher(fd,
"BruteForce",
os.path.join(imagePath, "matches.txt"),
forceRun=True)
print(Chain.Render(fm, 'openCV.txt'))
def imageConvertChain(imagePath):
imageSource = Sources.ImageSource(imagePath, "jpg")
imageConvert = Sources.ImageConvert(imageSource, imagePath, "pgm")
print Chain.Render(imageConvert,"UnitTest-imageConvertChain-log.txt")
import Chain
import random
blocks = [Chain.GenesisBlock(name='Main', password='******', block_id=str(10))]
previous_digest = blocks[0].compute_hash()
for i in range(0, 10):
random_id = 10
block = Chain.Block(name='Prasanna',
password='******',
previous_hash=previous_digest,
bolck_id=str(random_id))
blocks.append(block)
previous_digest = block.compute_hash()
hashes = [i.getPreviousHash() for i in blocks[1:]]
print(hashes)
#check integrity of any block:
block_number = 5
#get hash of the block 5 and that hash is stored in 5+1th block , for any n block, n+1 block has its hash
#hash of that block
previous_digest = blocks[block_number + 1].getPreviousHash()
#block:
block = blocks[block_number]
#check integrity:
def insert_chain_novacoin(store):
import Chain
store.insert_chain(Chain.create("NovaCoin"))
def performRender(self, stageObject):
print
print Chain.Render(stageObject,"log.txt")
# Copyright (c) 2012, Adam J. Rossi. All rights reserved. See README for licensing details.
import sys, os
sys.path.append(os.path.abspath("."))
import Chain # Chain must be imported first, requirement of registry
import Sources, FeatureExtraction, FeatureMatch, BundleAdjustment, Cluster, Common
# path to images / PMVS
imagePath = os.path.abspath("../Datasets/ET")
pmvsPath = os.path.join(imagePath, "pmvs")
# build chain
imageSourceJpg = Sources.ImageSource(imagePath, "jpg")
imageSource = Sources.ImageConvert(imageSourceJpg, imagePath, "pgm")
asift = FeatureExtraction.ASIFT(imageSource)
keyMatch = FeatureMatch.ASIFTMatch(asift)
bundler = BundleAdjustment.Bundler([keyMatch, imageSource])
radialUndistort = Cluster.RadialUndistort([bundler, imageSourceJpg])
prepCmvsPmvs = Cluster.PrepCmvsPmvs(radialUndistort, pmvsPath)
cmvs = Cluster.CMVS(prepCmvsPmvs)
pmvs = Cluster.PMVS(cmvs)
# render chain
print Chain.Render(pmvs, "asift.txt")
def insert_chain_novacoin(store):
import Chain
try:
store.insert_chain(Chain.create("NovaCoin"))
except Exception:
pass
def insert_chain_novacoin(store):
import Chain
store.insert_chain(Chain.create("NovaCoin"))
def insert_chain_novacoin(store):
import Chain
try:
store.insert_chain(Chain.create("NovaCoin"))
except Exception:
pass
L[1].r = mat([0, -1.054, 0]) L[2].r = mat([0, 0, -6.447]) L[3].r = mat([0, 0.092, -0.054]) L[4].r = mat([0, 0, 0.566]) L[5].r = mat([0, 0, 1.554]) L[0].I = mat([0.276, 0.255, 0.071, 0, 0, 0]) L[1].I = mat([0.108, 0.018, 0.100, 0, 0, 0]) L[2].I = mat([2.51, 2.51, 0.006, 0, 0, 0]) L[3].I = mat([0.002, 0.001, 0.001, 0, 0, 0]) L[4].I = mat([0.003, 0.003, 0.0004, 0, 0, 0]) L[5].I = mat([0.013, 0.013, 0.0003, 0, 0, 0]) L[0].Jm = 0.953 L[1].Jm = 2.193 L[2].Jm = 0.782 L[3].Jm = 0.106 L[4].Jm = 0.097 L[5].Jm = 0.020 L[0].G = 1 L[1].G = 1 L[2].G = 1 L[3].G = 1 L[4].G = 1 L[5].G = 1 qz = [0, 0, 0, 0, 0, 0] stanf = Chain(L, name='Stanford arm')
