def kmeans(self, pixelcluster=True):
'''
calculates kmeans centers for the cob from the centers of the kernels it contains
'''
if pixelcluster == True:
pixellist = []
for kernel in self.kernellist:
pixellist.extend(kernel.pixellist)
kmeans = Kernel.KMeans(n_clusters=2).fit(pixellist)
else:
kmeans = Kernel.KMeans(n_clusters=2).fit(self.kernelcenters)
meanc1 = kmeans.cluster_centers_[0].tolist()
meanc2 = kmeans.cluster_centers_[1].tolist()
sizec1 = 0
sizec2 = 0
kernelclusters = []
for kernel in self.kernellist:
for cluster in kernel.clusters:
kernelclusters.append(cluster)
for label, cluster in zip(kmeans.labels_, kernelclusters):
if label == 0:
sizec1 += cluster[0]
elif label == 1:
sizec2 += cluster[0]
self.clusters.append([sizec1, meanc1])
self.clusters.append([sizec2, meanc2])
def _LSSVMtrain(X, Y, kernel_dict, regulator):
m = Y.shape[0]
# Kernel
if kernel_dict['type'] == 'RBF':
K = Kernel.RBF(m, kernel_dict['gamma'])
K.calculate(X)
elif kernel_dict['type'] == 'LINEAR':
K = Kernel.LINEAR(m)
K.calculate(X)
elif kernel_dict['type'] == 'POLY':
K = Kernel.POLY(m, kernel_dict['c'], kernel_dict['d'])
K.calculate(X)
elif kernel_dict['type'] == 'TANH':
K = Kernel.TANH(m, kernel_dict['c'], kernel_dict['d'])
K.calculate(X)
elif kernel_dict['type'] == 'TL1':
K = Kernel.TL1(m, kernel_dict['rho'])
K.calculate(X)
H = np.multiply(np.dot(np.matrix(Y).T, np.matrix(Y)), K.kernelMat)
M_BR = H + np.eye(m) / regulator
#Concatenate
L_L = np.concatenate((np.matrix(0), np.matrix(Y).T), axis=0)
L_R = np.concatenate((np.matrix(Y), M_BR), axis=0)
L = np.concatenate((L_L, L_R), axis=1)
R = np.ones(m + 1)
R[0] = 0
#solve
b_a = LA.solve(L, R)
b = b_a[0]
alpha = b_a[1:]
#return
return (alpha, b, K)
def setColorStats(self):
replineCenters = self.getReplineCenters()
LMean = 0
aMean = 0
bMean = 0
numberOfCobs = 0
for cob in self.cobs:
LMean += self.cobs[cob].averageLab["L"]
aMean += self.cobs[cob].averageLab["a"]
bMean += self.cobs[cob].averageLab["b"]
numberOfCobs += 1
LMean = LMean / float(numberOfCobs)
aMean = aMean / float(numberOfCobs)
bMean = bMean / float(numberOfCobs)
rgb1 = Kernel.HunterLabToRGB(replineCenters[0][0],
replineCenters[0][1],
replineCenters[0][2])
rgb2 = Kernel.HunterLabToRGB(replineCenters[1][0],
replineCenters[1][1],
replineCenters[1][2])
self.averageRGB["R"], self.averageRGB["G"], self.averageRGB[
"B"] = Kernel.HunterLabToRGB(LMean, aMean, bMean)
self.averageLab["L"] = LMean
self.averageLab["a"] = aMean
self.averageLab["b"] = bMean
self.centers = {"R1": rgb1["R"], "R2": rgb2["R"], "G1": rgb1["G"], "G2": rgb2["G"], "B1": rgb1["B"], "B2": rgb2["B"],
"L1": replineCenters[0][0], "L2": replineCenters[1][0], "a1": replineCenters[0][1], "a2": replineCenters[1][1], "b1": replineCenters[0][2], "b2": replineCenters[1][2]}
clusterDifference = (abs(replineCenters[0][0] - replineCenters[1][0]) +
abs(replineCenters[0][1] - replineCenters[1][1]) +
abs(replineCenters[0][2] - replineCenters[1][2]))
class KernelTestCase(unittest.TestCase):
def runTest(self):
self.kernel = Kernel()
self.console = Console()
self.i1 = Instruction(1)
self.i2 = Instruction(2)
self.program = Program("p1")
self.program.inst.append(self.i1)
self.program.inst.append(self.i2)
self.kernel.run(self.program,self.console)
self.assertEqual(self.program.inst[1],self.console.instructions[1])
def instructionNumberTest(self):
self.i1 = Instruction(1)
self.assertEqual(self.i1.number,1)
def addConsoleTest(self):
self.kernel = Kernel()
self.console = Console()
self.i1 = Instruction(1)
self.i2 = Instruction(2)
self.program = Program("p1")
self.program.inst.append(self.i1)
self.program.inst.append(self.i2)
self.kernel.run(self.program,self.console)
self.assertEqual(self.program.inst,self.console.instructions)
def _KSVMtrain(X, Y, kernel_dict):
m = Y.shape[0]
if kernel_dict['type'] == 'RBF':
K = Kernel.RBF(m, kernel_dict['gamma'])
K.calculate(X)
elif kernel_dict['type'] == 'LINEAR':
K = Kernel.LINEAR(m)
K.calculate(X)
elif kernel_dict['type'] == 'POLY':
K = Kernel.POLY(m)
K.calculate(X)
elif kernel_dict['type'] == 'TANH':
K = Kernel.TANH(m, kernel_dict['c'], kernel_dict['d'])
K.calculate(X)
elif kernel_dict['type'] == 'TL1':
K = Kernel.TL1(m, kernel_dict['rho'])
K.calculate(X)
p1, p2 = trans_mat(K.kernelMat)
K.kernelMat = np.dot((p1 - p2), K.kernelMat)
#根据SVM求出alpha,b ？？？
svm = Algorithms.SVM(X, Y, kernel_dict)
#更新alpha
alpha = np.dot((p1 - p2), svm.alphas)
b = svm.b
return (alpha, b, K)
def getReplineCenters(self, graph=False, mean=False, size = False):
kernelcenters = []
for cob in xrange(len(self.cobs.keys())):
kernelcenters.extend(self.getCob(cob+1).KernelsCenters)
KM = KMeans(n_clusters=2, n_init=20).fit(kernelcenters)
kmeans = KM.cluster_centers_
if graph == True:
l, a, b = [], [], []
for x in kernelcenters:
l.append(x[0])
a.append(x[1])
b.append(x[2])
ax = Kernel.showScatterPlot(l, a, b)
Kernel.addpoints(kmeans, ax, color='r', marker='o')
if mean == True:
labMean = []
labMean.append((self.averageLab["L"], self.averageLab["a"],
self.averageLab["b"]))
Kernel.addpoints(labMean, ax, color='g', marker='o')
if size == True:
size1 = 0
size2 = 0
for x in KM.labels_:
if x == 0:
size1 += 1
elif x == 1:
size2 += 1
return KM, size1, size2
return np.array(kmeans)
def showscatterplot(self, s=80, closepreviousplot=True):
if len(self.coblist) == 1:
self.coblist[0].showscatterplot(s, closepreviousplot)
else:
lablists = Kernel.threeTupleToThreeLists(self.allkernelclusters)
if closepreviousplot == True:
plt.close(1)
plot = plt.figure()
axes = plot.add_subplot(111, projection='3d')
llist = lablists[0]
alist = lablists[1]
blist = lablists[2]
for l, a, b in zip(llist, alist, blist):
R, G, B = Kernel.HunterLabToRGB(l, a, b, normalized=True)
axes.scatter(l, a, b, color=[R, G, B], marker='s', s=s)
axes.set_xlabel('L')
axes.set_ylabel('a')
axes.set_zlabel('b')
totalsize = 0
for cluster in self.clusters:
totalsize += cluster[0]
for cluster in self.clusters:
addedsize = int(s * (cluster[0] / totalsize))
s += addedsize
Kernel.addpoints(cluster[1], axes, marker="o", color="g", s=s)
plt.title(self.name)
plt.ion()
plt.show()
return axes
def fit(self, X, Y):
# print('Kernel:', kernel_dict)
train_data = np.append(X, Y.reshape(len(Y), 1), axis=1)
if self.databalance == 'LowSampling':
data_maj = train_data[Y == 1] # 将多数
data_min = train_data[Y != 1]
index = np.random.randint(len(data_maj), size=len(data_min))
lower_data_maj = data_maj[list(index)]
train_data = np.append(lower_data_maj, data_min, axis=0)
X = train_data[:, :-1]
Y = train_data[:, -1]
self.Y = Y
elif self.databalance == 'UpSampling':
X, Y = SVMSMOTE(random_state=42).fit_sample(train_data[:, :-1],\
np.asarray(train_data[:, -1]))
self.Y = Y
else:
X = X
Y = Y
self.Y = Y
m = Y.shape[0]
# Kernel
if self.kernel_dict['type'] == 'RBF':
K = Kernel.RBF(m, self.kernel_dict['sigma'])
elif self.kernel_dict['type'] == 'LINEAR':
K = Kernel.LINEAR(m)
elif self.kernel_dict['type'] == 'POLY':
K = Kernel.POLY(m, self.kernel_dict['d'])
K.calculate(X)
tmp1 = np.hstack((np.ones((1, 2 * m)), [[0]]))
M_BR = K.kernelMat + np.eye(m) / (self.C * self.m_value)
tmp2 = np.hstack((M_BR, K.kernelMat, np.ones((m, 1))))
M_BL = K.kernelMat + np.eye(m) / (self.C * (1 - self.m_value))
tmp3 = np.hstack((K.kernelMat, M_BL, np.ones((m, 1))))
L = np.vstack((tmp1, tmp2, tmp3))
R = np.ones(2 * m + 1)
R[0] = 0
R[m + 1:] = -1
# solve
solution = LA.solve(L, R)
b = solution[-1]
alpha = solution[:m]
beta = solution[m:2 * m]
print('b', b)
# self.gamma = gamma
self.beta = beta
self.alpha = alpha
self.b = b
self.K = K
self.kernelMat = K.kernelMat
def fit(self, X, Y):
# print('Kernel:', self.kernel_dict)
train_data = np.append(X, Y.reshape(len(Y), 1), axis=1)
if self.databalance == 'LowSampling':
data_maj = train_data[Y == 1] # 将多数
data_min = train_data[Y != 1]
index = np.random.randint(len(data_maj), size=len(data_min))
lower_data_maj = data_maj[list(index)]
train_data = np.append(lower_data_maj, data_min, axis=0)
X = train_data[:, :-1]
Y = train_data[:, -1]
self.Y = Y
elif self.databalance == 'UpSampling':
X, Y = SVMSMOTE(random_state=42).fit_sample(train_data[:, :-1],\
np.asarray(train_data[:, -1]))
self.Y = Y
else:
X = X
Y = Y
self.Y = Y
m = len(Y)
# Kernel
if self.kernel_dict['type'] == 'RBF':
K = Kernel.RBF(m, self.kernel_dict['sigma'])
K.calculate(X)
elif self.kernel_dict['type'] == 'LINEAR':
K = Kernel.LINEAR(m)
K.calculate(X)
elif self.kernel_dict['type'] == 'POLY':
K = Kernel.POLY(m, self.kernel_dict['d'])
K.calculate(X)
H = np.multiply(np.dot(np.matrix(Y).T, np.matrix(Y)), K.kernelMat)
M_BR = H + np.eye(m) / (self.C)
# Concatenate
L_L = np.concatenate((np.matrix(0), np.matrix(Y).T), axis=0)
L_R = np.concatenate((np.matrix(Y), M_BR), axis=0)
L = np.concatenate((L_L, L_R), axis=1)
R = np.ones(m + 1)
R[0] = 0
# solve
b_a = LA.solve(L, R)
b = b_a[0]
alpha = b_a[1:]
e = alpha / self.C
self.alpha = alpha
self.b = b
self.K = K
self.kernelMat = K.kernelMat
return self.alpha, self.b, e
def dbscan(self, eps=.5, plot=False):
if len(self.coblist) > 1:
pixlist = []
totalnumkernels = 0
for cob in self.coblist:
for kernel in cob.kernellist:
pixlist.extend(kernel.pixellist)
totalnumkernels += 1
X = Kernel.np.array(pixlist)
density = eps
numberofpixels = len(pixlist)
db = Kernel.DBSCAN(eps=density).fit(X)
core_samples_mask = Kernel.np.zeros_like(db.labels_, dtype=bool)
core_samples_mask[db.core_sample_indices_] = True
labels = db.labels_
n_clusters_ = len(set(labels)) - (1 if -1 in labels else 0)
unique_labels = set(labels)
colors = []
for k in unique_labels:
class_member_mask = (labels == k)
xyz = X[class_member_mask & core_samples_mask]
llist, alist, blist = xyz[:, 0], xyz[:, 1], xyz[:, 2]
if len(llist) >= numberofpixels / 100:
lmean = llist.mean()
amean = alist.mean()
bmean = blist.mean()
self.clusters.append([size, [lmean, amean, bmean]])
r, g, b = Kernel.HunterLabToRGB(lmean, amean, bmean)
colors.append([r / 255.0, g / 255.0, b / 255.0])
else:
colors.append('k')
if plot is True:
graph = plt.figure()
ax = graph.add_subplot(111, projection='3d')
for k, col in zip(unique_labels, colors):
if k == -1:
col = 'k'
class_member_mask = (labels == k)
xyz = X[class_member_mask & core_samples_mask]
if len(xyz[:, 0]) >= numberofpixels / 100:
print len(xyz[:, 0])
ax.scatter(xyz[:, 0], xyz[:, 1], xyz[:, 2], c=col)
xyz = X[class_member_mask & ~core_samples_mask]
ax.scatter(xyz[:, 0],
xyz[:, 1],
xyz[:, 2],
c=col,
marker='.')
ax.set_xlabel('L')
ax.set_ylabel('a')
ax.set_zlabel('b')
plt.title('Estimated number of clusters: %d' % n_clusters_)
plt.ion()
plt.show()
return db
elif len(self.coblist) == 1:
self.clusters = self.coblist[0].clusters
def TablicaF2(X, Y, mp, wsp, F0, WarP):
for Ele in range(le):
Out = Przylozdo1(X, Y, mp[Ele], wsp, Ele)
if (Out == true):
# print("Przyłożono do Ele nr: ", Ele)
w1, w2, w3, w4 = mp[Ele]
F0 = KE.ObciazenieP(F0, WarP / 4, w1 - 1)
F0 = KE.ObciazenieP(F0, WarP / 4, w2 - 1)
F0 = KE.ObciazenieP(F0, WarP / 4, w3 - 1)
F0 = KE.ObciazenieP(F0, WarP / 4, w4 - 1)
return F0
def main():
interaction_kernel_0 = Kernel.GaussKernel(3)
interaction_kernel_0.add_mode(1.0, [0.5, 0.5, 0.5], [0.0, 0.0, 0.0])
interaction_kernel_0.add_mode(-5.5, [5.5, 5.5, 5.5], [0.0, 0.0, 0.0])
interaction_kernel_0.calculate()
interaction_kernel_1 = Kernel.GaussKernel(1)
interaction_kernel_1.add_mode(1.0, [0.5], [0.0])
interaction_kernel_1.add_mode(-5.5, [5.5], [0.0])
interaction_kernel_1.calculate()
input_field = DynamicField.DynamicField([[5], [2]], [], None)
input_field.set_boost(20)
blub = numpy.array([[0.0, 0.5, 1.0, 0.5, 0.0], [0.0, 0.25, 0.5, 0.25,
0.0]])
blub = blub.transpose() * 40
input_weight = DynamicField.Weight(blub)
field_0 = DynamicField.DynamicField([[5], [4], [2]], [], None)
field_1 = DynamicField.DynamicField([[4], [6], [10]], [], None)
scaler = DynamicField.Scaler()
# weight = DynamicField.Weight([0., 0.5, 1.0, 0.5, 0.0])
# weight = DynamicField.Weight(5.)
projection_0 = DynamicField.Projection(2, 2, set([0, 1]), [1, 0])
processing_steps = [scaler]
DynamicField.connect(field_0, field_1, processing_steps)
#DynamicField.connect(input_field, field_0, [input_weight])
for i in range(0, 500):
# input_field.step()
# input_weight.step()
field_0.step()
print("field 0:")
print(field_0.get_output())
print(field_0.get_output().shape)
for processing_step in processing_steps:
processing_step.step()
print(processing_step.get_name() + ": ")
print(processing_step.get_output())
print(processing_step.get_output().shape)
field_1.step()
print("field 1:")
print(field_1.get_activation())
print(field_1.get_activation().shape)
def convolute(self, kernel, fourier=None):
"""
The implement of convolution.
It will choose a better algorithm to do it depends on the size of kernel and image.
:param kernel:
:param fourier:Whether use fourier transform to calculate the convolution
:return:
"""
if not isinstance(kernel, Kernel.Kernel):
try:
kernel = Kernel.Kernel(kernel)
except Exception:
raise Exception('The input must be a kernel')
kernel_size = kernel.shape[0] * kernel.shape[1]
image_size = np.sqrt(self.shape[0] * self.shape[1])
if fourier is not None:
if fourier:
return self.__fourier_convolution(kernel)
else:
return self.__base_convolution(kernel)
# According to the Mark Nixon's book(p.87 3rd version),If m² < 4*log(N) + 1,
# then we should use direct implementation, otherwise the fourier transform should be considered.
else:
if kernel_size < 4 * np.log(image_size) + 1:
return self.__base_convolution(kernel)
else:
return self.__fourier_convolution(kernel)
def filter(image,depth,kernel_type,kernel_size):
kernel=Kernel.kernel(kernel_type,kernel_size)
depth=int(depth)
dst = cv2.filter2D(image, depth, kernel)
return dst
def drawScatterPlot(self, cob=1, kernel=0, pixelsPerKernel=100):
c = self.getCob(cob)
k = c.kernelList[kernel]
r, g, B, l, a, b = self.getkernelcolorlists(
cob=cob, kernel=kernel, pixelsPerKernel=pixelsPerKernel)
# return Kernel.showScatterPlot(r,g,B)
return Kernel.showScatterPlot(l, a, b)
def simulink(self,data,modelInputPath,col=50):
tf.reset_default_graph()
batch = 1
row = 1
channel = 1
# label container
label = tf.placeholder(tf.float32, shape=[1, 1])
# input data container
input = tf.placeholder(tf.float32, shape=[batch, row, col, channel], name='input')
filterKernel = kernel.averageFilter(shape=[3, 1, 1, 1]);
# convlution
conv2dRel = tf.nn.conv2d(input, filter=filterKernel, strides=[1, 1, 1, 1], data_format='NHWC', padding='SAME')
# pooling
maxpoolRel = tf.nn.max_pool(conv2dRel, ksize=[1, 3, 3, 1], strides=[1, 1, 1, 1], padding='SAME',
data_format='NHWC')
deminsion = maxpoolRel.shape.as_list()
# reshape
maxPoolFlat = tf.reshape(maxpoolRel, shape=[1, deminsion[0] * deminsion[1] * deminsion[2] * deminsion[3]])
# Hidden layer
hiddenW = tf.Variable(np.zeros(shape=[deminsion[0] * deminsion[1] * deminsion[2] * deminsion[3],
deminsion[0] * deminsion[1] * deminsion[2] * deminsion[3]],
dtype=np.float32), name='Hidden')
hiddenBias = tf.Variable(np.zeros(shape=[1], dtype=np.float32), name='HiddenBias')
Hidden = tf.nn.sigmoid(tf.matmul(maxPoolFlat, hiddenW) + hiddenBias)
# output layer
W = tf.Variable(
np.zeros(shape=[deminsion[0] * deminsion[1] * deminsion[2] * deminsion[3], 1], dtype=np.float32),
dtype=tf.float32, name='W')
rel = tf.sigmoid(tf.matmul(Hidden, W) + tf.Variable(np.zeros(shape=[1], dtype=np.float32), name='OutputBias'));
# define the loss function
loss = tf.losses.mean_squared_error(labels=label, predictions=rel)
# init all the weight value
init = tf.global_variables_initializer()
# begin training process
with tf.Session() as sess:
saver = tf.train.Saver(write_version=tf.train.SaverDef.V2) # use this save the network model
# save the data for using tensorboard show the network structure
# tf.summary.FileWriter("G:/GraduationDesignModelData/logs/", sess.graph)
sess.run(init)
# restore the all kinds of network weights to the cnn network
# print('\033[1;32;47m', end='')
print("\t\t\tmodel file restore from path : " + modelInputPath)
saver.restore(sess=sess, save_path=modelInputPath)
inputData = inda.getInputData([batch, row, col, channel])
for jj in range(len(data)):
inputData[0][0][jj][0] = data[jj]
predictValue=sess.run(rel,feed_dict={input:inputData})
return predictValue[0][0]
def TablicaF(X, Y, mp, wsp, F0, WarP):
for Ele in range(le):
Out = Przylozdo1(X, Y, mp[Ele], wsp, Ele)
if (Out == true):
print("Przyłożono do Ele nr: ", Ele, " o War", WarP)
F0 = KE.ObciazenieP(F0, WarP, Ele)
return F0
def setupSystem(scu):
import os
import zephyr.Kernel as Kernel
from IPython.parallel.error import UnmetDependency
global localSystem
global localLocator
tag = (scu['ifreq'], scu['iky'])
# If there is already a system to do this job on this machine, push the duplicate to another
if tag in localSystem:
raise UnmetDependency
subSystemConfig = baseSystemConfig.copy()
subSystemConfig.update(scu)
# Set up method output caching
if 'cacheDir' in baseSystemConfig:
subSystemConfig['cacheDir'] = os.path.join(
baseSystemConfig['cacheDir'], 'cache', '%d-%d' % tag)
localSystem[tag] = Kernel.SeisFDFDKernel(subSystemConfig,
locator=localLocator)
return tag
def __init__(self, kernels, show=False):
'''
TEST THIS
'''
self.name = ''
self.averageRGB = {"R": 0, "G": 0, "B": 0}
self.averageLab = {"L": 0, "a": 0, "b": 0}
self.kernelList = kernels
self.numberOfKernels = len(self.kernelList)
LMean = 0
aMean = 0
bMean = 0
#The below code will calculate the 2SDMean wrong!
for kernel in self.kernelList:
LMean += kernel.LabDict["L2SDMean"]
aMean += kernel.LabDict["a2SDMean"]
bMean += kernel.LabDict["b2SDMean"]
LMean = LMean / float(self.numberOfKernels)
aMean = aMean / float(self.numberOfKernels)
bMean = bMean / float(self.numberOfKernels)
# the above code is wrong!
rgb = Kernel.HunterLabToRGB(LMean, aMean, bMean)
self.averageRGB["R"] = rgb["R"]
self.averageRGB["G"] = rgb["G"]
self.averageRGB["B"] = rgb["B"]
self.averageLab["L"] = LMean
self.averageLab["a"] = aMean
self.averageLab["b"] = bMean
self.KernelsCenters = []
self.setKernelsCenters()
def kmeans(self):
'''
calculates kmeans centers for the repline from the centers of the cobs it contains
'''
if len(self.coblist) > 1:
allkernelsizes = []
self.allkernelclusters = []
for cob in self.coblist:
for kernel in cob.kernellist:
for cluster in kernel.clusters:
allkernelsizes.append(cluster[0])
self.allkernelclusters.append(cluster[1])
kmeans = Kernel.KMeans(n_clusters=2).fit(self.allkernelclusters)
meanc1 = kmeans.cluster_centers_[0].tolist()
meanc2 = kmeans.cluster_centers_[1].tolist()
sizec1 = 0
sizec2 = 0
for label, size in zip(kmeans.labels_, allkernelsizes):
if label == 0:
sizec1 += size
elif label == 1:
sizec2 += size
self.clusters.append([sizec1, meanc1])
self.clusters.append([sizec2, meanc2])
self.checkdistance()
else:
self.segregating = self.coblist[0].segregating
self.clusters = self.coblist[0].clusters
def simulink(self, inputData, inputNum, lstmCellNum, outputNum,
modelInputPath):
tf.reset_default_graph()
everyLstmCellNums = 400
label = tf.placeholder(tf.float32, shape=[None, outputNum])
predictValue = []
# input data container
input = tf.placeholder(tf.float32,
shape=[None, 1, inputNum, 1],
name='input')
filterKernel = kernel.kernelA(shape=[1, 3, 1, 1])
# convlution
conv2dRel = tf.nn.conv2d(input,
filter=filterKernel,
strides=[1, 1, 1, 1],
data_format='NHWC',
padding='SAME')
# pooling
maxpoolRel = tf.nn.max_pool(conv2dRel,
ksize=[1, 1, 3, 1],
strides=[1, 1, 3, 1],
padding='SAME',
data_format='NHWC')
demensions = maxpoolRel.shape.as_list()
####0:batch,1H,2W,3C
maxPoolRelFlat = tf.reshape(maxpoolRel, shape=[-1, demensions[2]])
listCells = []
for i in range(lstmCellNum):
listCells.append(rnn.BasicLSTMCell(everyLstmCellNums))
rnn_cell = rnn.MultiRNNCell(listCells)
outputs, states = tf.nn.static_rnn(rnn_cell, [maxPoolRelFlat],
dtype=tf.float32)
predict = tf.layers.dense(inputs=outputs[0], units=outputNum)
predict = tf.nn.sigmoid(predict, name="predict")
init = tf.global_variables_initializer()
with tf.Session() as sess:
saver = tf.train.Saver(write_version=tf.train.SaverDef.V2
) # use this save the network model
# save the data for using tensorboard show the network structure
# tf.summary.histogram("W",W)
sess.run(init)
print("\t\t\tmodel file restore from path : " + modelInputPath)
saver.restore(sess=sess, save_path=modelInputPath)
predictValue = sess.run(predict, feed_dict={input: inputData})
return predictValue
def gradient(image,kernel_type,kernel_size):
if image is None:
print 'Error in input Image'
return 0
kernel=Kernel.kernel(kernel_type,kernel_size)
gradient = cv2.morphologyEx(image, cv2.MORPH_GRADIENT, kernel)
return gradient
def close(image,kernel_type,kernel_size):
if image is None:
print 'Error in input Image'
return 0
kernel=Kernel.kernel(kernel_type,kernel_size)
closing = cv2.morphologyEx( image, cv2.MORPH_CLOSE, kernel )
return closing
def drawScatterPlotWithCenters(self, cob=1, kernel=0, pixelsPerKernel=100, x='', y='', z=''):
if x != '' and y != '' and z != '':
l = x
a = y
b = z
lab = []
for i in xrange(len(x)):
lab.append((x[i], y[i], z[i]))
else:
c = self.getCob(cob)
k = c.kernelList[kernel]
R, G, B, l, a, b = self.getkernelcolorlists(
cob=cob, kernel=kernel, pixelsPerKernel=pixelsPerKernel)
lab = k.getlabTupleList()
kmeans = KMeans(n_clusters=2).fit(lab).cluster_centers_
ax = Kernel.showScatterPlot(l, a, b)
Kernel.addpoints(kmeans, ax, color='r', marker='o')
return kmeans
def Blackhat(image,kernel_type,kernel_size):
if image is None:
print 'Error in input Image'
return 0
kernel=Kernel.kernel(kernel_type,kernel_size)
blackhat = cv2.morphologyEx(image, cv2.MORPH_BLACKHAT, kernel)
return blackhat
def getReplineCenters(self, graph=False, mean=False):
kernelcenters = []
for cob in xrange(len(self.cobs.keys())):
kernelcenters.append(self.clustersList(cob=(cob + 1)))
KM = KMeans(n_clusters=2).fit(kernelcenters[0])
kmeans = KM.cluster_centers_
if graph == True:
l, a, b = [], [], []
for x in kernelcenters[0]:
l.append(x[0])
a.append(x[1])
b.append(x[2])
ax = Kernel.showScatterPlot(l, a, b)
Kernel.addpoints(kmeans, ax, color='r', marker='o')
if mean == True:
labMean = (self.averageLab["L"], self.averageLab["a"],
self.averageLab["b"])
Kernel.addpoints(labMean, ax, color='g', marker='o')
return np.array(kmeans)
def runTest(self):
self.kernel = Kernel()
self.console = Console()
self.i1 = Instruction(1)
self.i2 = Instruction(2)
self.program = Program("p1")
self.program.inst.append(self.i1)
self.program.inst.append(self.i2)
self.kernel.run(self.program,self.console)
self.assertEqual(self.program.inst[1],self.console.instructions[1])
def createcobs(self, clustertype="kmeans", stats=False):
'''
looks at all the files in self.directory and finds and with the same base name as self.name.
each file is turned into a cob object, and add to self.cobs
'''
for cobfile in os.listdir(self.directory):
if '_' + self.name + "." in cobfile:
filenamewithoutlastextension = os.path.splitext(cobfile)[0]
basename = os.path.splitext(filenamewithoutlastextension)[0]
kernellist = []
with open(self.directory + "/" + cobfile) as csvfile:
csvreader = csv.reader(csvfile)
csvlist = list(csvreader)
listofpixels = []
currentkernel = 1
for line in csvlist[:-1]:
try:
if line[0] == 'Image':
pass
elif int(line[1]
) != currentkernel and line[4] != '':
kernellist.append(
Kernel.Kernel(listofpixels,
name=currentkernel,
clustertype="dbscan",
stats=stats))
listofpixels = []
currentkernel = int(line[1])
currentpixel = [
int(line[2]),
int(line[3]),
int(line[4])
]
listofpixels.append(currentpixel)
elif int(line[1]) == currentkernel:
currentpixel = [
int(line[2]),
int(line[3]),
int(line[4])
]
listofpixels.append(currentpixel)
except Exception, e:
print str(e), "in create cobs"
IndexError
currentcob = Cob.Cob(kernellist,
basename,
pixelcluster=False,
clustertype=clustertype,
stats=stats)
print "Finished Cob: ", basename
self.coblist.append(currentcob)
def checkdistance(self):
c1 = self.clusters[0]
c2 = self.clusters[1]
dist = Kernel.clusterdistance(c1[1], c2[1])
if dist < 7.5:
L = (c1[0] * c1[1][0] + c2[0] * c2[1][0]) / (c1[0] + c2[0])
a = (c1[0] * c1[1][1] + c2[0] * c2[1][1]) / (c1[0] + c2[0])
b = (c1[0] * c1[1][2] + c2[0] * c2[1][2]) / (c1[0] + c2[0])
self.clusters = []
self.clusters.append([c1[0] + c2[0], [L, a, b]])
self.segregating = False
else:
self.segregating = True
return dist
def medianblur(image, kernel_type,kernel_size):
if image is None:
print 'Error in input Image'
return 0
cv2.Laplacian(image,cv2.CV_8U)
kernel=Kernel.kernel(kernel_type,kernel_size)
medBlur = cv2.medianBlur(image, kernel)
return medblur
def get_change(self, activation=None, use_time_scale=True):
"""Compute the next change to the system. By default, the current value
of the field is used, but a different value can be supplied to compute
the output for an arbitrary value. When use_time_scale is set to False,
the time scale is not considered when computing the change."""
# get the current output of the dynamic field
current_output = self.get_output()
# if a specific current activation is supplied..
if activation is not None:
# .. compute the output given this activation
current_output = self.get_output(activation)
else:
# ..otherwise set the activation to the current value of the field
activation = self._activation
# if the time scale is to be used..
if use_time_scale is True:
# ..compute the inverse of the time scale to have a factor..
relaxation_time_factor = 1. / self._relaxation_time
else:
# ..otherwise, set the factor to one
relaxation_time_factor = 1.
# compute the lateral interaction
lateral_interaction = 0.
if self._lateral_interaction_kernels is not None:
for kernel in self._lateral_interaction_kernels:
lateral_interaction += Kernel.convolve(current_output, kernel)
# sum up the input coming in from all connected fields
field_interaction = 0
for connectable in self.get_incoming_connectables():
field_interaction += connectable.get_output()
global_inhibition = self._global_inhibition * current_output.sum(
) / math_tools.product(self._output_dimension_sizes)
# generate the noise term
noise = self._noise_strength * numpy.random.normal(
0.0, self._noise_standard_deviation, self._output_dimension_sizes)
# compute the change of the system
change = relaxation_time_factor * (
-self._normalization_factor * activation + self._resting_level +
self._boost - global_inhibition + lateral_interaction +
field_interaction + noise)
return change
def testTuples():
assertEqual(Tuple.pair(1,2), Tuple.pair(1,2))
assertTrue(Kernel.eq(Tuple.pair(1,2), Tuple.pair(1,2)))
assertFalse(Kernel.eq(Tuple.pair(1,2), Tuple.pair(3,4)))
t = Tuple.pair(5, 6)
assertEqual(Tuple.first(t), 5)
assertEqual(Tuple.second(t), 6)
assertEqual(
Tuple.mapFirst(double, t),
(10, 6))
assertEqual(
Tuple.mapSecond(double, t),
(5, 12))
assertEqual(
Tuple.mapBoth(triple, double, t),
(15, 12))
assertEqual(
toPy(Tuple.mapFirst(F(List.cons)(0), toElm(([1], [2])))),
([0, 1], [2]))
def showscatterplot(self, s=20, closepreviousplot=True):
'''
creates a 3d scatter plot whose points are either pixels from all the kernels in this cob,
or centers from the kmean clusters of each kernel in this cob.
'''
if self.type == 'pixels':
pixels = []
for kernel in self.kernellist:
pixels.extend(kernel.pixellist)
lablists = Kernel.threeTupleToThreeLists(pixels)
else:
lablists = Kernel.threeTupleToThreeLists(self.kernelcenters)
if closepreviousplot == True:
plt.close(1)
plot = plt.figure()
axes = plot.add_subplot(111, projection='3d')
llist = lablists[0]
alist = lablists[1]
blist = lablists[2]
for l, a, b in zip(llist, alist, blist):
R, G, B = Kernel.HunterLabToRGB(l, a, b, normalized=True)
axes.scatter(l, a, b, color=[R, G, B], marker='s', s=s)
axes.set_xlabel('L')
axes.set_ylabel('a')
axes.set_zlabel('b')
totalsize = 0
for cluster in self.clusters:
totalsize += cluster[0]
for cluster in self.clusters:
addedsize = int(s * (cluster[0] / totalsize))
s += addedsize
Kernel.addpoints(cluster[1], axes, marker="o", color="g", s=s)
plt.title(self.name)
plt.ion()
plt.show()
return axes
def low_pass_filter(self, sigma, size=None, fourier=None):
"""
Filter implemented by Gaussian Kernel
:param fourier:
:param sigma: int, should be 1.0, 1.5 or anything else
:param size: size of the kernel
:return:
"""
if size:
size = size
else:
size = int(8 * sigma + 1)
low_filter_kernel = Kernel.GaussianKernel(size, sigma)
self.low_pass = self.convolute(low_filter_kernel, fourier=fourier)
self.low_pass.img_name = self.img_name + ' low-pass filter'
return self.low_pass
def setKernelsandRGB(self, show=False):
'''
For each entry in self.cobs, it will open the file with that name in repDirectory.
The file is a csv file of the format "accessionName, Kernel, R, G, B". This function will return a list of
ints that correspond to the number of kernels that are associated with the Cob file.
'''
print "Creating Kernels and Pixels"
progressBar = 0
for key in self.cobs:
progressBar += 1
kernelList = []
filePath = self.repDirectory + "/" + key + ".tif.csv"
with open(filePath) as csvFile:
csvReader = csv.reader(csvFile)
csvList = list(csvReader)
print "Cob: ", progressBar, "/", len(self.cobs)
listofpixels = []
currentKernel = 1
for line in csvList:
try:
if line[0] == 'Image':
pass
elif int(line[1]) != currentKernel and line[4] != '':
kernelList.append(
Kernel.Kernel(listofpixels,
name=currentKernel))
if show == True:
print "Kernel: %s" % currentKernel
listofpixels = []
currentKernel = int(line[1])
currentPixel = Pixel.Pixel(int(line[2]),
int(line[3]),
int(line[4]))
listofpixels.append(currentPixel)
elif int(line[1]) == currentKernel:
currentPixel = Pixel.Pixel(int(line[2]),
int(line[3]),
int(line[4]))
listofpixels.append(currentPixel)
except:
IndexError
self.cobs[key] = Cob.Cob(kernelList)
print "Kernel's Initialized for %s" % key
print "All Cob's Initialized"
def fit(self, touchData, targetsAreOffsets=False):
"""
Fits the model to the given training data.
Parameters:
touchData - 2D array, each row is one touch with intended target, with columns touch x and y, and target x and y
targetsAreOffsets - boolean, defaults to false; if true, the 3rd and 4th column of each row in the touchData array
are interpreted as measured offsets directly, instead of target locations
Returns:
This method has no return value.
"""
inputs = np.matrix(touchData[:, 0:2])
if not targetsAreOffsets:
targetsX = np.matrix(touchData[:, 2] - touchData[:, 0]).T
targetsY = np.matrix(touchData[:, 3] - touchData[:, 1]).T
else:
targetsX = np.matrix(touchData[:, 2]).T
targetsY = np.matrix(touchData[:, 3]).T
self.targetsX = targetsX
self.targetsY = targetsY
'Stack targets:'
self.targets = np.vstack((targetsX, targetsY))
'Create design matrix:'
n, m = np.shape(inputs)
self.mX = np.matrix(inputs)
'Create covariance matrix / kernel:'
mC = Kernel.createMixedKernel(self.mX, self.mX, self.gamma,
self.kernelMix)
mC_stacked_left = np.vstack((mC, mC * self.diag))
mC_stacked_right = np.vstack((mC * self.diag, mC))
mC_stacked = np.hstack((mC_stacked_left, mC_stacked_right))
mC_stacked_noised = mC_stacked + np.identity(2 * n) * self.noiseVar
self.mC_chol = splin.cho_factor(mC_stacked_noised)[0]
self.mC_inv_mult_targets = splin.cho_solve((self.mC_chol, False),
self.targets)
def gaussianFilter(image, kernel_type,kernel_size, sigmaX, sigmaY):
if image is None:
print 'Error in input Image'
return 0
kernel_size=Point.point_int(kernel_size)
if sigmaY==0 and sigmaX==0:
sigmaX=kernel_size[0]
sigmaY=kernel_size[1]
kernel=Kernel.kernel(kernel_type,kernel_size)
sigmaColor = int(sigmaX)
sigmaSpace = int(sigmaY)
if kernel_size[0]%2==0 and kernel_size[1]%2==0:
print 'The kernel size should be odd'
return 0
image=cv2.GaussianBlur(image,kernel_size , sigmaColor, sigmaSpace)
return image
def main(self):
memoria = Memory()
file_system = FileSystem()
kernel = Kernel(memoria, file_system)
kernel.execute()
def train(self, C=[0.01, 1, 10, 100], tol=1e-3):
m = self.Y.shape[0]
A = [0] * 10
B = [0] * 10
indices = numpy.random.permutation(
self.X.shape[0]) # shape[0]表示第0轴的长度，通常是训练数据的数量
rand_data_x = self.X[indices]
rand_data_y = self.Y[indices] # data_y就是标记（label）
l = int(len(indices) / 10)
for i in range(9):
A[i] = rand_data_x[i * l:i * l + l]
B[i] = rand_data_y[i * l:i * l + l]
A[9] = rand_data_x[9 * l:]
B[9] = rand_data_y[9 * l:]
# '''
# X_num=self.X.shape[0]
# train_index=range(X_num)
# test_size=int(X_num*0.1)+1
# for i in range(9):
# test_index=[]
# for j in range(test_size):
# randomIndex=int(numpy.random.uniform(0,len(train_index)))
# test_index.append(train_index[randomIndex])
# #del train_index[randomIndex]
# A[i]=self.X[test_index,:]
# B[i]=self.Y[test_index,:]
# A[9]=self.X.ix_[train_index]
# B[9]=self.Y.ix_[train_index]
# '''
acc_best = 0
C_best = None
avg_acc = 0
# gamma_best = None
for CVal in C:
# for gammaVal in gamma:
# avg_acc = 0
for i in range(10):
X_test = A[i]
Y_test = B[i]
# X_train = None
# Y_train = None
#model= SMO.SMO_Model(X_train, Y_train, CVal, kernel,gammaVal, tol=1e-3, eps=1e-3)
#output_model=SMO.SMO(model)
#根据output_model的参数信息计算对应decision_function----->推得accuracy
#acc = _evaulate(output_model)
X_train = numpy.concatenate([
A[(i + 1) % 10], A[(i + 2) % 10], A[(i + 3) % 10],
A[(i + 4) % 10], A[(i + 5) % 10], A[(i + 6) % 10],
A[(i + 7) % 10], A[(i + 8) % 10], A[(i + 9) % 10]
],
axis=0)
Y_train = numpy.concatenate([
B[(i + 1) % 10], B[(i + 2) % 10], B[(i + 3) % 10],
B[(i + 4) % 10], B[(i + 5) % 10], B[(i + 6) % 10],
B[(i + 7) % 10], B[(i + 8) % 10], B[(i + 9) % 10]
],
axis=0)
# SMO.GG = gammaVal
# calculate Kernel Matrix then pass it to SMO.
if self.IK:
if self.kernel_dict['type'] == 'TANH':
K = Kernel.TANH(X_train.shape[0],
self.kernel_dict['c'],
self.kernel_dict['d'])
K.calculate(X_train)
elif self.kernel_dict['type'] == 'TL1':
K = Kernel.TL1(X_train.shape[0],
self.kernel_dict['rho'])
K.calculate(X_train)
p1, p2 = trans_mat(K.kernelMat)
K.kernelMat = np.dot((p1 - p2), K.kernelMat)
if self.kernel_dict['type'] == 'RBF':
K = Kernel.RBF(X_train.shape[0], self.kernel_dict['gamma'])
K.calculate(X_train)
elif self.kernel_dict['type'] == 'LINEAR':
K = Kernel.LINEAR(X_train.shape[0])
K.calculate(X_train)
elif self.kernel_dict['type'] == 'POLY':
K = Kernel.POLY(X_train.shape[0], self.kernel_dict['c'],
self.kernel_dict['d'])
K.calculate(X_train)
elif self.kernel_dict['type'] == 'TANH':
K = Kernel.TANH(X_train.shape[0], self.kernel_dict['c'],
self.kernel_dict['d'])
K.calculate(X_train)
elif self.kernel_dict['type'] == 'TL1':
K = Kernel.TL1(X_train.shape[0], self.kernel_dict['rho'])
K.calculate(X_train)
model = SMO.SMO_Model(X_train,
Y_train,
CVal,
K,
tol=1e-3,
eps=1e-3)
output_model = SMO.SMO(model)
#IK
if self.IK:
output_model.alphas = np.dot((p1 - p2),
output_model.alphas)
acc = SMO._evaluate(output_model, X_test, Y_test)
avg_acc = avg_acc + acc / 10
if avg_acc > acc_best:
acc_best = avg_acc
#更新C gamma
C_best = CVal
# gamma_best =gammaVal
# self.gamma = gamma_best
#最后一遍train
# SMO.GG = gamma_best
#!K
if self.IK:
if self.kernel_dict['type'] == 'TANH':
K = Kernel.TANH(self.X.shape[0], self.kernel_dict['c'],
self.kernel_dict['d'])
K.calculate(self.X)
elif self.kernel_dict['type'] == 'TL1':
K = Kernel.TL1(self.X.shape[0], self.kernel_dict['rho'])
K.calculate(self.X)
p1, p2 = trans_mat(K.kernelMat)
K.kernelMat = np.dot((p1 - p2), K.kernelMat)
if self.kernel_dict['type'] == 'RBF':
K = Kernel.RBF(self.X.shape[0], self.kernel_dict['gamma'])
K.calculate(self.X)
elif self.kernel_dict['type'] == 'LINEAR':
K = Kernel.LINEAR(self.X.shape[0])
K.calculate(self.X)
elif self.kernel_dict['type'] == 'POLY':
K = Kernel.POLY(self.X.shape[0], self.kernel_dict['c'],
self.kernel_dict['d'])
K.calculate(self.X)
elif self.kernel_dict['type'] == 'TANH':
K = Kernel.TANH(self.X.shape[0], self.kernel_dict['c'],
self.kernel_dict['d'])
K.calculate(self.X)
elif self.kernel_dict['type'] == 'TL1':
K = Kernel.TL1(self.X.shape[0], self.kernel_dict['rho'])
K.calculate(self.X)
SVM_model = SMO.SMO(
SMO.SMO_Model(self.X, self.Y, C_best, K, tol=1e-3, eps=1e-3))
# 参数传递给最后生成的SVM类
if self.IK:
SVM_model.alphas = np.dot((p1 - p2), SVM_model.alphas)
self.X = SVM_model.X
self.Y = SVM_model.y
self.kernel_dict = SVM_model.kernel
self.alphas = SVM_model.alphas
self.b = SVM_model.b
# C_best = C
# gamma_best =gamma
# (w,b) = SMO(X_train,Y_train,C_best,gamma_best,kernal,tol=1e-3)
# self.w = w
# self.b = b
return None
def f_Golden(y, x_glob, x_loc, y_off, coords, mType, wType,criterion, maxVal, minVal, tol, maxIter=200,flag=0):
"""
Golden section search
Arguments
----------
y : array
n*1, dependent variable.
x_glob : array
n*k1, fixed independent variable.
x_local : array
n*k2, local independent variable, including constant.
y_off : array
n*1, offset variable for Poisson model
coords : dictionary
including (x,y) coordinates involved in the weight evaluation (including point i)
mType : integer
GWR model type, 0: Gaussian, 1: Poisson, 2: Logistic
wType : integer
kernel type, 0: fix_Gaussian, 1: adap_Gaussian, 2: fix_Bisquare, 3: adap_Bisquare
criterion : integer
bandwidth selection criterion, 0: AICc, 1: AIC, 2: BIC, 3: CV
maxVal : float
maximum value used in bandwidth searching
minVal : float
minimum value used in bandwidth searching
tol : float
tolerance used to determine convergence
maxIter : integer
maximum number of iteration if convergence cannot arrive at the tolerance
flag : integer
distance type
Return:
opt_band : float
optimal bandwidth
opt_weit : kernel
optimal kernel
output : list of tuple
report searching process, keep bandwidth and score, [(bandwidth, score),(bandwidth, score),...]
"""
dist = Kernel.get_pairDist(coords,flag) #get pairwise distance between points
# 1 set range of bandwidth
if x_glob is None:
nVar_glob = 0
else:
nVar_glob = len(x_glob[0])
if x_loc is None:
nVar_loc = 0
else:
nVar_loc = len(x_loc[0])
nVars = nVar_glob + nVar_loc
a,c = ini_band_dist(dist, nVars, wType, maxVal, minVal)
# 2 get initial b value
output = []
lamda = 0.38197 #1 - (np.sqrt(5.0)-1.0)/2.0
# get b and d
b = a + lamda * abs(c-a) #distance or nn based on wType
d = c - lamda * abs(c-a) # golden section
if wType == 1 or wType == 3: # bandwidth is nn
b = round(b,0)
d = round(d,0)
# 3 loop
pre_opt = 0.0
diff = 1.0e9
nIter = 0
while abs(diff) > tol and nIter < maxIter:
nIter += 1
# 3.1 create kernel
weit_a = Kernel.GWR_W(coords, a, wType, dist)
weit_b = Kernel.GWR_W(coords, b, wType, dist)
weit_c = Kernel.GWR_W(coords, c, wType, dist)
weit_d = Kernel.GWR_W(coords, d, wType, dist)
# 3.2 decide whether local model or mixed model
if x_glob is None: # local model
#if mType == 0: #mType == 0 or
#gwrMod_a = GWR_Gaussian_Base(y, x_loc, weit_a)
#gwrMod_b = GWR_Gaussian_Base(y, x_loc, weit_b)
#gwrMod_c = GWR_Gaussian_Base(y, x_loc, weit_c)
#gwrMod_d = GWR_Gaussian_Base(y, x_loc, weit_d)
#else:
gwrMod_a = GWGLM_Base(y, x_loc, weit_a, mType, y_off)
gwrMod_b = GWGLM_Base(y, x_loc, weit_b, mType, y_off)
gwrMod_c = GWGLM_Base(y, x_loc, weit_c, mType, y_off)
gwrMod_d = GWGLM_Base(y, x_loc, weit_d, mType, y_off)
else: # mixed model
gwrMod_a = semiGWR_Base(y, x_glob, x_loc, weit_a, mType, y_off)
gwrMod_b = semiGWR_Base(y, x_glob, x_loc, weit_b, mType, y_off)
gwrMod_c = semiGWR_Base(y, x_glob, x_loc, weit_c, mType, y_off)
gwrMod_d = semiGWR_Base(y, x_glob, x_loc, weit_d, mType, y_off)
# 3.3 get diagnostic value(0: AICc, 1: AIC, 2: BIC, 3: CV)
if mType == 0:#or mType == 3
f_a = getDiag_GWR[criterion](gwrMod_a)
f_b = getDiag_GWR[criterion](gwrMod_b)
f_c = getDiag_GWR[criterion](gwrMod_c)
f_d = getDiag_GWR[criterion](gwrMod_d)
else:
f_a = getDiag_GWGLM[criterion](gwrMod_a)
f_b = getDiag_GWGLM[criterion](gwrMod_b)
f_c = getDiag_GWGLM[criterion](gwrMod_c)
f_d = getDiag_GWGLM[criterion](gwrMod_d)
#print "a: %.3f, b: %.3f, c: %.3f, d: %.3f" % (a, b, c, d)
# determine next triple
if f_b <= f_d:
# current optimal bandwidth
opt_weit = weit_b
opt_band = b
opt_cri = f_b
c = d
d = b
b = a + lamda * abs(c-a)
if wType == 1 or wType == 3: # bandwidth is nn
b = round(b,0)
else:
# current optimal bandwidth
opt_weit = weit_d
opt_band = d
opt_cri = f_d
a = b
b = d
d = c - lamda * abs(c-a)
if wType == 1 or wType == 3: # bandwidth is nn
d = round(d,0)
output.append((opt_band,opt_cri))
# determine diff
diff = f_b - f_d #opt_cri - pre_opt
pre_opt = opt_cri
#print "diff: %.6f" % (diff)
return opt_band, opt_weit, output
def f_Interval(y, x_glob, x_loc, y_off, coords, mType, wType, criterion, maxVal, minVal, interval,flag=0):
"""
Interval search, using interval as stepsize
Arguments
----------
y : array
n*1, dependent variable.
x_glob : array
n*k1, fixed independent variable.
x_local : array
n*k2, local independent variable, including constant.
y_off : array
n*1, offset variable for Poisson model
coords : dictionary
including (x,y) coordinates involved in the weight evaluation (including point i)
mType : integer
GWR model type, 0: M_Gaussian, 1: M_Poisson, 2: Logistic
wType : integer
kernel type, 0: fix_Gaussian, 1: adap_Gaussian, 2: fix_Bisquare, 3: adap_Bisquare
criterion : integer
bandwidth selection criterion, 0: AICc, 1: AIC, 2: BIC, 3: CV
maxVal : float
maximum value used in bandwidth searching
minVal : float
minimum value used in bandwidth searching
interval : float
interval used in interval search
flag : integer
distance type
Return:
opt_band : float
optimal bandwidth
opt_weit : kernel
optimal kernel
output : list of tuple
report searching process, keep bandwidth and score, [(bandwidth, score),(bandwidth, score),...]
"""
dist = Kernel.get_pairDist(coords,flag=0) #get pairwise distance between points
a = minVal
c = maxVal
# add codes to check whether a and c are valid
#------------------------------------------------------------
if wType == 1 or wType == 3: # bandwidth is nn
a = int(a)
c = int(c)
output = []
# 1 get initial b value
b = a + interval #distance or nn based on wType
if wType == 1 or wType == 3: # bandwidth is nn
b = int(b)
# 2 create weight
weit_a = Kernel.GWR_W(coords, a, wType, dist)
weit_c = Kernel.GWR_W(coords, c, wType, dist)
# 3 create model
if x_glob is None: # local model
#if mType == 3:
#gwrMod_a = GWR_Gaussian(y, x_loc, weit_a)
#gwrMod_c = GWR_Gaussian(y, x_loc, weit_c)
#else:
gwrMod_a = GWGLM_Base(y, x_loc, weit_a, mType, y_off)
gwrMod_c = GWGLM_Base(y, x_loc, weit_c, mType, y_off)
else: # mixed model
gwrMod_a = semiGWR_Base(y, x_glob, x_loc, weit_a, mType, y_off)
gwrMod_c = semiGWR_Base(y, x_glob, x_loc, weit_c, mType, y_off)
# 4 get diagnostic value
if mType == 0:#or mType == 3
f_a = getDiag_GWR[criterion](gwrMod_a)
f_c = getDiag_GWR[criterion](gwrMod_c)
else:
f_a = getDiag_GWGLM[criterion](gwrMod_a)
f_c = getDiag_GWGLM[criterion](gwrMod_c)
# 5 add to the output
output.append((a,f_a))
output.append((c,f_c))
#print "bandwidth: %.3f, f value: %.6f" % (a, f_a)
#print "bandwidth: %.3f, f value: %.6f" % (c, f_c)
if f_a < f_c:
opt_weit = weit_a
opt_band = a
opt_val = f_a
else:
opt_weit = weit_c
opt_band = c
opt_val = f_c
while b < c:
# model using bandwidth b
weit_b = Kernel.GWR_W(coords, b, wType, dist) # local model
if x_glob is None: # local model
#if mType == 3:
#gwrMod_b = GWR_Gaussian(y, x_loc, weit_b)
#else:
gwrMod_b = GWGLM_Base(y, x_loc, weit_b, mType, y_off)
else: # mixed model
gwrMod_b = semiGWR_Base(y, x_glob, x_loc, weit_b, mType, y_off)
if mType == 0:#or mType == 3
f_b = getDiag_GWR[criterion](gwrMod_b)
else:
f_b = getDiag_GWGLM[criterion](gwrMod_b)
#print "bandwidth: %.3f, f value: %.6f" % (b, f_b)
# add output
output.append((b,f_b))
# determine next triple
if f_b < opt_val:
opt_weit = weit_b
opt_band = b
opt_val = f_b
# update b
b = b + interval
return opt_band,opt_weit, output
def pred(data, refData, band, y, x_local, y_hat=None, wType=0, mType=0, flag=0, y_offset=None, sigma2=1, y_fix=None, fMatrix=None):
"""
predict values at unsampled locations
Arguments:
data : dictionary,
(x,y) of unsampled locations
refData : dictionary,
(x,y) of sampled locations
band : float
bandwidth
y : array
n*1, dependent variable
y_hat : array
n*1, predicted y from original model, to calculate local statistics
x_local : array
n*k1, local independent variable
y_offset : array
n*1, offset variable for Poisson model
sigma2 : float
used to calculate std. error of betas for Gaussian model
y_fix : array
n*1, fixed part of y from global Xs, used in mixed model
fMatrix : array
n*n, hat matrix for global model, used in mixed model
wType : integer
define which kernel function to use
mType : integer
model type, model type, 0: Gaussian, 1: Poisson, 2: Logistic
flag : dummy,
0 or 1, 0: Euclidean distance; 1: spherical distance
Return:
Betas : array
n*k, Beta estimation
std_err : array
n*k, standard errors of Beta
t_stat : array
n*k, local t-statistics
localR2 : array
n*1, local R square or local p-dev
"""
# 1 get W matrix
dicDist = {}
n_pred = len(data.keys())
for i in range(n_pred):# calculate distance between unsampled obs and sampled obs
dicDist[i] = Kernel.get_focusDist(data[i], refData, flag)
weit = Kernel.GWR_W(data, band, wType, dicDist)
#print len(dicDist[0].keys())
#print len(weit.w.keys())
#print len(weit.w[0])
# 2 get predicted local Beta estimation
#if mType == 0:# 2.1 basic Gaussian
#mod_loc = GWR_Gaussian_Base(y, x_local, weit)
#else:# 2.2 GWGLM models including mixed models
mod_loc = GWGLM_Base(y, x_local, weit, mType, y_offset, y_fix, fMatrix)
pred_betas = mod_loc.Betas[:n_pred]
# 3 get std errors of Betas
#if mType == 1 or mType == 2:
#sigma2 = 1.0
pred_stdErr = np.sqrt(mod_loc.CCT * sigma2)
# 4 get t statistics
pred_tstat = pred_betas/pred_stdErr
# 5 get local R2 or local p-dev
localR2 = np.zeros(shape=(n_pred,1))
n_reg = len(y)
if mType == 0 : # Gaussian model or mType == 3
for i in range(n_pred):
w_i= np.reshape(np.array(weit.w[i]), (-1, 1))
sum_yw = np.sum(y * w_i)
ybar = 1.0 * sum_yw / np.sum(w_i)
rss = np.sum(w_i * (y - y_hat)**2)
tss = np.sum(w_i * (y - ybar)**2)
localR2[i] = (tss - rss)/tss
if mType == 1: # Poisson model
for i in range(n_pred):
w_i= np.reshape(np.array(weit.w[i]), (-1, 1))
sum_yw = np.sum(y * w_i)
ybar = 1.0 * sum_yw / np.sum(w_i * y_offset)
dev = 0.0
dev0 = 0.0
for j in range(n_reg):
if y[j] <>0:
dev += 2 * y[j] * (np.log(y[j]) - np.log(y_hat[j])) * w_i[j]
dev0 += 2 * y[j] * (np.log(y[j]) - np.log(ybar * y_offset[j])) * w_i[j]
dev -= 2 * (y[j] - y_hat[j]) * w_i[j]
dev0 -= 2 * (y[j] - ybar * y_offset[j]) * w_i[j]
localR2[i] = 1.0 - dev / dev0
if mType == 2: # Logistic model
for i in range(n_pred):
w_i= np.reshape(np.array(weit.w[i]), (-1, 1))
sum_yw = np.sum(y * w_i)
ybar = 1.0 * sum_yw / np.sum(w_i)
dev = 0.0
dev0 = 0.0
for j in range(n_reg):
if (1.0 - y_hat[j] < 1e-10):
nu = np.log(y_hat[j]/1e-10)
dev += -2* (y[j] * nu + np.log(1e-10) ) * w_i[j]
else:
nu = np.log(y_hat[j]/(1.0 - y_hat[j]))
dev += -2* (y[j] * nu + np.log(1.0 - y_hat[j])) * w_i[j]
nu0 = np.log(ybar/(1-ybar))
dev0 += -2* (y[j] * nu0 + np.log(1.0 - ybar) ) * w_i[j]
localR2[i] = 1.0 - dev / dev0
return pred_betas, pred_stdErr, pred_tstat, localR2
Programa5.add(IoInstruccion1)
Programa5.add(IoInstruccion5)
Programa5.add(CpuInstruccion4)
myCDROM = CDROM()
myPrinter = Printer()
myMMU = MMU()
myDiskWithPrograms = Disk()
myDiskWithPrograms.load(Programa1)
myDiskWithPrograms.load(Programa2)
myDiskWithPrograms.load(Programa3)
myDiskWithPrograms.load(Programa4)
myDiskWithPrograms.load(Programa5)
myEmptyDisk = Disk()
asignacionContinua = AsignacionContinua(PrimerAjuste(),myMMU)
myMMU.setLogicalMemory(asignacionContinua)
#myKernel = Kernel(Fifo, myMMU, myEmptyDisk)
myKernel = Kernel(Fifo, myMMU, myDiskWithPrograms)
myKernel.addDevice(myCDROM)
myKernel.addDevice(myPrinter)
myKernel.initializeThread()
myKernel.runProcess("Programa1")
myKernel.runProcess("Programa2")
myKernel.runProcess("Programa3")
myKernel.runProcess("Programa4")
myKernel.runProcess("Programa5")
# Definimos un Disco
hdd = HardDisk()
hdd.save(program1)
hdd.save(program2)
hdd.save(program3)
# Definimos el Sistema de I/O
iosys = IOSystem()
iosys.addDevice(hdd)
# Definimos la CPU con un quantum de 3
cpu = CPU()
# Definimos el Kernel
kernel1point0 = Kernel()
# Definimos la Memoria
pageTable = PageTable()
memory = Memoria(300,pageTable)
# Definimos el Manejador de Interrupciones
IH = InterruptionHandler(iosys,memory,pageTable,kernel1point0,cpu)
# Seteamos el IH en todos los modulos que haga falta
cpu.setInterruptionHandler(IH)
kernel1point0.setInterruptionHandler(IH)
# creamos el shell
shell = Shell("123",IH)
# print "I am %s" % self.name
if re.match("J", self.jiang):
self.jiang = self.jiang[1:]
import temp
file = open("temp.py", "w")
file.write("from test import " + self.jiang + "\n\n\ndef jiang():\n"+"\t" + self.jiang + "()\n")
# file = open("temp.py", "r")
file.close()
reload(temp)
temp.jiang()
else:
print(self.jiang)
if __name__ == "__main__":
k = Kernel()
k.bootstrap(learnFiles=["en1.6/jiang.aiml", "self-test.aiml"])
lock = threading.Lock()
print "\nEntering interactive mode (ctrl-c to exit)"
i = 0
while True:
jiang = k.respond(raw_input("> "))
my_thread = MyThread(jiang=jiang)
my_thread.start()
# print "current has %d threads" % (threading.activeCount())
ThA = threading.enumerate()
for d in range(len(ThA)):
print ThA[d]
i += 1
print i