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What happens if you specify an index that is too high?
beatles[7]
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
How can you know how long a list is?
len(beatles)
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
Do remember that indexing starts at 0, so don't make the mistake of thinking that len(yourlist) will give you the last item of your list!
beatles[len(beatles)]
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
This will work!
beatles[len(beatles) -1]
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
If-statements Most of the times, what you want to do when you program is to check a value and execute some operation depending on whether the value matches some condition. That's where if statements help! In its easiest form, an If statement is syntactic construction that checks whether a condition is met; if it is som...
bassist = "Paul McCartney" if bassist == "Paul McCartney": print("Paul played bass with the Beatles!")
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
Mind the indentation very much! This is the essential element in the syntax of the statement
bassist = "Bill Wyman" if bassist == "Paul McCartney": print("I'm part of the if statement...") print("Paul played bass in the Beatles!")
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
What happens if the condition is not met? Nothing! The indented code is not executed, because the condition is not met, so lines 4 and 5 are simply skipped. But what happens if we de-indent line 5? Can you guess why this is what happes? Most of the time, we need to specify what happens if the conditions are not met
bassist = "" if bassist == "Paul McCartney": print("Paul played bass in the Beatles!") else: print("This guy did not play for the Beatles...")
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
This is the flow: * the condition in line 3 is checked * is it met? * yes: then line 4 is executed * no: then line 6 is executed Or we can specify many different conditions...
bassist = "Bill" if bassist == "Paul McCartney": print("Paul played bass in the Beatles!") elif bassist == "Bill Wyman": print("Bill Wyman played for the Rolling Stones!") else: print("I don't know what band this guy played for...")
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
For loops The greatest thing about lists is that thet are iterable, that is you can loop through them. What do we do if we want to apply some line of code to each element in a list? Try with a for loop! A for loop can be paraphrased as: "for each element named x in an iterable (e.g. a list): do some code (e.g. print th...
for b in beatles: print(b + " was one of the Beatles")
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
Let's break the code down to its parts: * b: an arbitrary name that we give to the variable holding every value in the loop (it could have been any name; b is just very convenient in this case!) * beatles: the list we're iterating through * : as in the if-statements: don't forget the colon! * indent: also, don't forget...
beatles = ["John", "Paul", "George", "Ringo"] for b in beatles: if b == "Paul": instrument = "bass" elif b == "John": instrument = "rhythm guitar" elif b == "George": instrument = "lead guitar" elif b == "Ringo": instrument = "drum" print(b + " played " + instrument +...
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
Input and Output One of the most frequent tasks that programmers do is reading data from files, and write some of the output of the programs to a file. In Python (as in many language), we need first to open a file-handler with the appropriate mode in order to process it. Files can be opened in: * read mode ("r") * wri...
#see? we assign the file-handler to a variable, or we wouldn't be able #to do anything with that! f = open("NOTES.md", "r")
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
note that "r" is optional: read is the default mode! Now there are a bunch of things we can do: * read the full content in one variable with this code: content = f.read() read the lines in a list of lines: lines = f.readlines() or, which is the easiest, simply read the content one line at the time with a for loop; t...
for l in f: print(l)
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
Once you're done, don't forget to close the handle:
f.close() #all together f = open("NOTES.md") for l in f: print(l) f.close()
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
Now, there's a shortcut statement, which you'll often see and is very convenient, because it takes care of opening, closing and cleaning up the mess, in case there's some error:
with open("NOTES.md") as f: #mind the indent! for l in f: #double indent, of course! print(l)
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
Now, how about writing to a file? Let's try to write a simple message on a file; first, we open the handler in write mode
out = open("test.txt", "w") #the file is now open; let's write something in it out.write("This is a test!\nThis is a second line (separated with a new-line feed)")
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
The file has been created! Let's check this out
#don't worry if you don't understand this code! #We're simply listing the content of the current directory... import os os.listdir()
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
But before we can do anything (e.g. open it with your favorite text editor) you have to close the file-handler!
out.close()
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
Let's look at its content
with open("test.txt") as f: print(f.read())
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
Again, also for writing we can use a with statement, which is very handy. But let's have a look at what happens here, so we understand a bit better why "write mode" must be used carefully!
with open("test.txt", "w") as out: out.write("Oooops! new content")
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
Let's have a look at the content of "test.txt" now
with open("test.txt") as f: print(f.read())
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
See? After we opened the file in "write mode" for the second time, all content of the file was erased and replaced with the new content that we wrote!!! So keep in mind: when you open a file in "w" mode: if it doesn't exist, a new file with that name is created if it does exist, it is completely overwritten and all pr...
with open("test.txt", "a") as out: out.write('''\nAnd this is some additional content. The new content is appended at the bottom of the existing file''') with open("test.txt") as f: print(f.read())
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
Functions Above, we have opened a file several times to inspect its content. Each time, we had to type the same code over and over. This is the typical case where you would like to save some typing (and write code that is much easier to maintain!) by defining a function A function is a block of reusable code that can b...
def printFileContent(file_name): #the function takes one argument: file_name with open(file_name) as f: print(f.read())
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
As usual, mind the indent! file_name (line 1) is the placeholder that we use in the function for any argument that we want to pass to the function in our real-life reuse of the code. Now, if we want to use our function we simply call it with the file name that we want to print out
printFileContent("README.md")
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
Now, let's see an example of a function that returns some value to the users. Those functions typically take some argument, process them and yield back the result of this processing. Here's the easiest example possible: a function that takes two numbers as arguments, sum them and returns the result.
def sumTwoNumbers(first_int, second_int): s = first_int + second_int return s #could be even shorter: def sumTwoNumbers(first_int, second_int): return first_int + second_int sumTwoNumbers(5, 6)
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
Most often, you want to assign the result returned to a variable, so that you can go on working with the results...
s = sumTwoNumbers(5,6) s * 2
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
Error and exceptions Things can go wrong, especially when you're a beginner. But no panic! Errors and exceptions are actually a good thing! Python gives you detailed reports about what is wrong, so read them carefully and try to figure out what is not right. Once you're getting better, you'll actually learn that you ca...
if 1 > 0: print("Well, we know that 1 is bigger than 0!")
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
Pretty clear, isn't it? What you get is an error a construct that is not grammatical in Python's syntax. Note that you're also told where (at what line, and at what point of the code) your error is occurring. That is not always perfect (there are cases where the problem is actually occuring before what Python thinks), ...
var = "bla bla" if var1: print("If you see me, then I was defined...")
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
You get an exception! The syntax of your code is right, but the execution met with a problem that caused the program to stop. Now, in your program, you can handle selected exception: this means that you can write your code in a way that the program would still be executed even if a certain exception is raised. Let's se...
printFileContent("file_that_is_not_there.txt")
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
We get a FileNotFoundError! Now, let's re-write the function so that this event (somebody uses the function with a wrong file name) is taken care of...
def printFileContent(file_name): #the function takes one argument: file_name try: with open(file_name) as f: print(f.read()) except FileNotFoundError: print("The file does not exist.\nNevertheless, I do like you, and I will print something to you anyway...") printFileContent("fi...
participants_notebooks/Sunoikisis - Named Entity Extraction 1a-GB.ipynb
mromanello/SunoikisisDC_NER
gpl-3.0
We first define a function to prepare the datas in the format of keras (theano). The function also reduces the size of the imagesfrom 100X100 to 32X32.
def prep_datas(xset,xlabels): X=list(xset) for i in range(len(X)): X[i]=resize(X[i],(32,32,1)) #reduce the size of the image from 100X100 to 32X32. Also flattens the color levels X=np.reshape(X,(len(X),1,32,32)) # reshape the liste to have the form required by keras (theano), ie (1,32,32) ...
Archiv_Session_Spring_2017/Exercises/05_aps_capcha.ipynb
peterwittek/qml-rg
gpl-3.0
We then load the training set and the test set and prepare them with the function prep_datas.
training_set, training_labels = im.load_images(path_train) test_set, test_labels = im.load_images(path_test) X_train,Y_train=prep_datas(training_set,training_labels) X_test,Y_test=prep_datas(test_set,test_labels)
Archiv_Session_Spring_2017/Exercises/05_aps_capcha.ipynb
peterwittek/qml-rg
gpl-3.0
Image before/after compression
i=11 plt.subplot(1,2,1) plt.imshow(training_set[i],cmap='gray') plt.subplot(1,2,2) plt.imshow(X_train[i][0],cmap='gray')
Archiv_Session_Spring_2017/Exercises/05_aps_capcha.ipynb
peterwittek/qml-rg
gpl-3.0
Lenet neural network
# import the necessary packages from keras.models import Sequential from keras.layers.convolutional import Convolution2D from keras.layers.convolutional import MaxPooling2D from keras.layers.core import Activation from keras.layers.core import Flatten from keras.layers.core import Dense from keras.optimizers import SGD...
Archiv_Session_Spring_2017/Exercises/05_aps_capcha.ipynb
peterwittek/qml-rg
gpl-3.0
We build the neural network and fit it on the training set
model = LeNet.build(width=32, height=32, depth=1, classes=2) opt = SGD(lr=0.01)#Sochastic gradient descent with learning rate 0.01 model.compile(loss="categorical_crossentropy", optimizer=opt,metrics=["accuracy"]) model.fit(X_train, Y_train, batch_size=10, nb_epoch=300,verbose=1) y_pred = model.predict_classes(X_test)...
Archiv_Session_Spring_2017/Exercises/05_aps_capcha.ipynb
peterwittek/qml-rg
gpl-3.0
We now compare with the real world images (with the deshear method)
real_world_set=[] for i in np.arange(1,73): filename=path+'images/real_world/'+str(i)+'.png' real_world_set.append(im.deshear(filename)) fake_label=np.ones(len(real_world_set),dtype='int32') X_real,Y_real=prep_datas(real_world_set,fake_label) y_pred = model.predict_classes(X_real)
Archiv_Session_Spring_2017/Exercises/05_aps_capcha.ipynb
peterwittek/qml-rg
gpl-3.0
with the labels of Peter
f=open(path+'images/real_world/labels.txt',"r") lines=f.readlines() result=[] for x in lines: result.append((x.split(' ')[1]).replace('\n','')) f.close() result=np.array([int(x) for x in result]) result[result>1]=1 plt.plot(y_pred,'o') plt.plot(2*result,'o') plt.ylim(-0.5,2.5);
Archiv_Session_Spring_2017/Exercises/05_aps_capcha.ipynb
peterwittek/qml-rg
gpl-3.0
下準備 データのインポート, 基礎統計量の表示
# csvをインポート df = pd.read_csv( 'odakyu-mansion.csv' ) # 基礎統計量を表示 print(df.describe())
応用統計/HW1/HW1.ipynb
myuuuuun/various
mit
家の向きは東, 西, 南, 北のダミー変数(0または1。南東の場合、南と東の両方に1)に分解し変換して、
# サンプルサイズ data_len = df.shape[0] # 家の向きはdummyに df['d_N'] = np.zeros(data_len, dtype=float) df['d_E'] = np.zeros(data_len, dtype=float) df['d_W'] = np.zeros(data_len, dtype=float) df['d_S'] = np.zeros(data_len, dtype=float) for i, row in df.iterrows(): for direction in ["N", "W", "S", "E"]: if direction in ...
応用統計/HW1/HW1.ipynb
myuuuuun/various
mit
欠損値は平均値で置き換える。
df = df.fillna(df.mean())
応用統計/HW1/HW1.ipynb
myuuuuun/various
mit
最小二乗法 被説明変数に与える影響の小さい説明変数を順に取り除いていく。具体的にはp > 0.05であるような説明変数を除いていく。 同時に、外れ値の考慮もする。 最小二乗法その1 説明変数13個で最小二乗法を実行すると、
# 定数項も加える X = sm.add_constant(df[['time', 'bus', 'walk', 'area', 'bal', 'kosuu', 'floor', 'tf', 'd_N', 'd_E', 'd_S', 'd_W', 'year']]) # 普通の最小二乗法 model = sm.OLS(df.price, X) results = model.fit() # 結果を表示 print(results.summary())
応用統計/HW1/HW1.ipynb
myuuuuun/various
mit
となる。 p値を見ると、kosuu, floorがほとんど無関係であるように見える。 kosuuには外れ値が1つある(kosuu=2080)ので、それを除いてみる。 最小二乗法その2 外れ値を除き、
print(df.loc[161]) df = df.drop(161)
応用統計/HW1/HW1.ipynb
myuuuuun/various
mit
再び最小二乗法を実行すると、
X = sm.add_constant(df[['time', 'bus', 'walk', 'area', 'bal', 'kosuu', 'floor', 'tf', 'd_N', 'd_E', 'd_S', 'd_W', 'year']]) model = sm.OLS(df.price, X) results = model.fit() print(results.summary())
応用統計/HW1/HW1.ipynb
myuuuuun/various
mit
やはりkosuu, floorのp値が大きいので、説明変数から除くと、 最小二乗法その3
X = sm.add_constant(df[['time', 'bus', 'walk', 'area', 'bal', 'tf', 'd_N', 'd_E', 'd_S', 'd_W', 'year']]) model = sm.OLS(df.price, X) results = model.fit() print(results.summary())
応用統計/HW1/HW1.ipynb
myuuuuun/various
mit
となる。さらに、balと南向き以外の方角のダミー変数を説明変数から除く。 最小二乗法その4
X = sm.add_constant(df[['time', 'bus', 'walk', 'area', 'tf', 'year', 'd_S']]) model = sm.OLS(df.price, X) results = model.fit() print(results.summary())
応用統計/HW1/HW1.ipynb
myuuuuun/various
mit
p値が大きい南向きのダミー変数d_E、築年数yearも説明変数から除く。 最小二乗法その5
X = sm.add_constant(df[['time', 'bus', 'walk', 'area', 'tf']]) model = sm.OLS(df.price, X) results = model.fit() print(results.summary())
応用統計/HW1/HW1.ipynb
myuuuuun/various
mit
p値が大きいtfを取り除く 最小二乗法その6
X = sm.add_constant(df[['time', 'bus', 'walk', 'area']]) model = sm.OLS(df.price, X) results = model.fit() print(results.summary())
応用統計/HW1/HW1.ipynb
myuuuuun/various
mit
修正済みR^2 = 0.783, F統計量のp値3.96e-59 を見ると、「新宿駅からの乗車時間」, 「バスの乗車時間」, 「徒歩時間」, 「部屋の広さ」の4つで十分に住宅価格を説明できていると考えられる。 最小二乗法1〜6と比較しても、AIC・BICは殆ど変わらないか、改善している。 あとは残差を検討して、誤差項に関する諸仮定が満たされているかをチェックする。 残差の分析 残差に関する仮定は: 誤差項の平均が0 誤差項の分散が一定 誤差項は互いに独立 誤差項は(少なくとも近似的には)正規分布に従う 誤差項と各説明変数の相関係数は0 であった。 ※全ての項目を厳密にチェックする方法を知らないので、出来る項目だけを確認し...
# 回帰に使った変数だけを抜き出す new_df = df.loc[:, ['price', 'time', 'bus', 'walk', 'area']] # 説明変数行列 exp_matrix = new_df.loc[:, ['time', 'bus', 'walk', 'area']] # 回帰係数ベクトル coefs = results.params # 理論価格ベクトル predicted = exp_matrix.dot(coefs[1:]) + coefs[0] # 残差ベクトル residuals = new_df.price - predicted # 残差をplot fig, ax = plt.subplo...
応用統計/HW1/HW1.ipynb
myuuuuun/various
mit
平均はほぼ0であり、グラフでも0付近に点が集中していることがわかる: 仮定1は満たす しかしながら、右側にいくつか外れ値が見える。右上の1点を除いて、再度回帰分析を行う。 最小二乗法その7
print(new_df.loc[12] ) new_df = new_df.drop(12) X = sm.add_constant(new_df[['time', 'bus', 'walk', 'area']]) model = sm.OLS(new_df.price, X) results = model.fit() print(results.summary()) # 説明変数行列 exp_matrix = new_df.loc[:, ['time', 'bus', 'walk', 'area']] # 回帰係数ベクトル coefs = results.params # 理論価格ベクトル predicted = exp_...
応用統計/HW1/HW1.ipynb
myuuuuun/various
mit
最小二乗法6の結果に比べ、ばらつきが均等になった。 次に、縦軸に残差、横軸に各説明変数の観測値をとって、残差のばらつきを見る。
# 残差をplot fig = plt.figure(figsize=(18, 10)) ax1 = plt.subplot(2, 2, 1) plt.plot(exp_matrix['time'], residuals, 'o', color='b', linewidth=1, label="residuals - time") plt.xlabel("time") plt.ylabel("residuals") plt.legend() ax2 = plt.subplot(2, 2, 2, sharey=ax1) plt.plot(exp_matrix['bus'], residuals, 'o', color='b', l...
応用統計/HW1/HW1.ipynb
myuuuuun/various
mit
Now let's investigate the mean and standard deviation for the binomial distribution further. The mean of a binomial distribution is simply: $$\mu=np$$ This intuitively makes sense, the average number of successes should be the total trials multiplied by your average success rate. Similarly we can see that the standard ...
import numpy as np # Set up a new example, let's say n= 10 coin flips and p=0.5 for a fair coin. n=10 p=0.5 # Set up n success, remember indexing starts at 0, so use n+1 x = range(n+1) # Now create the probability mass function Y = binom.pmf(x,n,p) #Show Y # Next we'll visualize the pmf by plotting it.
notebooks/machineLearning_notebooks/01_Naive_Bayes/Distributions.ipynb
jamesfolberth/NGC_STEM_camp_AWS
bsd-3-clause
Finally we will plot the binomial distribution.
import matplotlib.pyplot as plt %matplotlib inline # For simple plots, matplotlib is fine, seaborn is unnecessary. # Now simply use plot plt.plot(x,Y,'o') #Title (use y=1.08 to raise the long title a little more above the plot) plt.title('Binomial Distribution PMF: 10 coin Flips, Odds of Success for Heads is p=0.5',...
notebooks/machineLearning_notebooks/01_Naive_Bayes/Distributions.ipynb
jamesfolberth/NGC_STEM_camp_AWS
bsd-3-clause
Looks awfully bell shaped... Going further Suppose you play a Blackjack, and have a 50\% chance of winning. You start with a 1 dollar bet, and if you lose, you double the amount you bet on the next play. So if you play three rounds, and Lose, Lose, Win, then you lost 1 dollar on the first round, 2 dollars on the second...
from IPython.display import Image Image(url='https://static.squarespace.com/static/549dcda5e4b0a47d0ae1db1e/54a06d6ee4b0d158ed95f696/54a06d70e4b0d158ed960413/1412514819046/1000w/Gauss_banknote.png')
notebooks/machineLearning_notebooks/01_Naive_Bayes/Distributions.ipynb
jamesfolberth/NGC_STEM_camp_AWS
bsd-3-clause
Now we define the normal pdf. The first equation below is the pdf for the normal distribution with mean $\mu$ and variance $\sigma^2$. The second equations is the standard normal $\Phi$ with mean $0$ and variance $1$. We can always transform our random variable $X \sim {\mathcal {N}}(\mu ,\,\sigma ^{2})$ to the standar...
#Import import matplotlib as mpl %matplotlib inline #Import the stats library from scipy import stats # Set the mean mn = 0 #Set the standard deviation std_dev = 1 # Create a range X = np.arange(-4,4,0.001) #Create the normal distribution for the range Y = stats.norm.pdf(X,mn,std_dev) # plt.plot(X,Y) from IPytho...
notebooks/machineLearning_notebooks/01_Naive_Bayes/Distributions.ipynb
jamesfolberth/NGC_STEM_camp_AWS
bsd-3-clause
The bell curve, centered at the mean, also shows the variance with how wide the bell is. The x-axis gives the realized values of the random variable, and the y values of the curve give the probability these values are realized by the random variable/experiment. This image does a great job of giving a good interpretatio...
#Set the mean and the standard deviaiton mu,sigma = 0,1 # Now grab 30 random numbers from the normal distribution norm_set = np.random.normal(mu,sigma,30) #Now let's plot it using seaborn import seaborn as sns import sklearn as sk from scipy.stats import gaussian_kde results, edges = np.histogram(norm_set, normed=Tr...
notebooks/machineLearning_notebooks/01_Naive_Bayes/Distributions.ipynb
jamesfolberth/NGC_STEM_camp_AWS
bsd-3-clause
With enough samples, this should start to look normal.
norm2 = np.random.normal(mu, sigma, 1000) results, edges = np.histogram(norm2, normed=True) binWidth = edges[1] - edges[0] plt.bar(edges[:-1], results*binWidth, binWidth) density = gaussian_kde(norm2) density.covariance_factor = lambda : .4 density._compute_covariance() plt.plot(X,density(X)) plt.plot(X,Y)
notebooks/machineLearning_notebooks/01_Naive_Bayes/Distributions.ipynb
jamesfolberth/NGC_STEM_camp_AWS
bsd-3-clause
Central Limit Theorem The Central Limit Theorem is one of the most important theorems in statistical theory. It states that when independent random variables are added, their sum tends toward a normal distribution even if the original variables themselves are not normally distributed. This may seem obscure so we will...
n10 = np.random.normal(mu, sigma, 10) n100 = np.random.normal(mu, sigma, 100) n1000 = np.random.normal(mu, sigma, 1000) n10000 = np.random.normal(mu, sigma, 10000) print(n10.mean(), n100.mean(), n1000.mean(), n10000.mean() )
notebooks/machineLearning_notebooks/01_Naive_Bayes/Distributions.ipynb
jamesfolberth/NGC_STEM_camp_AWS
bsd-3-clause
We see that as we add more samples, the mean approaches 0, which is the true mean. This is the central limit theorem: the sum of a lot of random variables tends towards a Gaussian distribution (under some conditions). The next image shows how adding more samples to a binomial distribution makes it look more and more Ga...
Image(url='https://upload.wikimedia.org/wikipedia/commons/8/8c/Dice_sum_central_limit_theorem.svg')
notebooks/machineLearning_notebooks/01_Naive_Bayes/Distributions.ipynb
jamesfolberth/NGC_STEM_camp_AWS
bsd-3-clause
Student's t distribution For the normal distribution it is often assumed that the sample size is assumed large ($N>30$). The t distribution allows for use of small samples, but does so by sacrificing certainty with a margin-of-error trade-off (i.e. a larger variance). The t distribution takes into account the sample si...
#Import for plots import matplotlib.pyplot as plt %matplotlib inline #Import the stats library from scipy.stats import t #import numpy import numpy as np # Create x range x = np.linspace(-5,5,100) # Create the t distribution with scipy rv = t(3) # Plot the PDF versus the x range plt.plot(x, rv.pdf(x)) plt.plot(X, ...
notebooks/machineLearning_notebooks/01_Naive_Bayes/Distributions.ipynb
jamesfolberth/NGC_STEM_camp_AWS
bsd-3-clause
Notice that the t distribution in blue has fatter tails than the normal distribution. This means there is more probability of realizing an observation in that region. As a consequence, there is less area under the peak/it is less spikey. This is a reflection of the fact that we have less certainty in where the observat...
import scipy.stats x, y = np.mgrid[-1:1:.01, -1:1:.01] pos = np.empty(x.shape + (2,)) pos[:, :, 0] = x; pos[:, :, 1] = y rv = scipy.stats.multivariate_normal([0.5, -0.2], [[2.0, 0.3], [0.3, 0.5]]) plt.contourf(x, y, rv.pdf(pos))
notebooks/machineLearning_notebooks/01_Naive_Bayes/Distributions.ipynb
jamesfolberth/NGC_STEM_camp_AWS
bsd-3-clause
Getting the data We're not going into details here
# Import the MNIST dataset mnist = input_data.read_data_sets("/tmp/MNIST/", one_hot=True) x_train = np.reshape(mnist.train.images, (-1, 28, 28, 1)) y_train = mnist.train.labels x_test = np.reshape(mnist.test.images, (-1, 28, 28, 1)) y_test = mnist.test.labels
code_samples/estimators-for-free/.ipynb_checkpoints/estimators_for_free-checkpoint.ipynb
mari-linhares/tensorflow-workshop
apache-2.0
Defining the input function If we look at the image above we can see that there're two main parts in the diagram, a input function interacting with data files and the Estimator interacting with the input function and checkpoints. This means that the estimator doesn't know about data files, it knows about input function...
BATCH_SIZE = 128 x_train_dict = {'x': x_train } train_input_fn = numpy_io.numpy_input_fn( x_train_dict, y_train, batch_size=BATCH_SIZE, shuffle=True, num_epochs=None, queue_capacity=1000, num_threads=4) x_test_dict = {'x': x_test } test_input_fn = numpy_io.numpy_input_fn( ...
code_samples/estimators-for-free/.ipynb_checkpoints/estimators_for_free-checkpoint.ipynb
mari-linhares/tensorflow-workshop
apache-2.0
Creating an experiment After an experiment is created (by passing an Estimator and inputs for training and evaluation), an Experiment instance knows how to invoke training and eval loops in a sensible fashion for distributed training. More about it here
# parameters LEARNING_RATE = 0.01 STEPS = 1000 # create experiment def generate_experiment_fn(): def _experiment_fn(run_config, hparams): del hparams # unused, required by signature. # create estimator model_params = {"learning_rate": LEARNING_RATE} estimator = tf.estimator.Estimator(model_fn=m.get_...
code_samples/estimators-for-free/.ipynb_checkpoints/estimators_for_free-checkpoint.ipynb
mari-linhares/tensorflow-workshop
apache-2.0
Run the experiment
OUTPUT_DIR = 'output_dir/model1' learn_runner.run(generate_experiment_fn(), run_config=tf.contrib.learn.RunConfig(model_dir=OUTPUT_DIR))
code_samples/estimators-for-free/.ipynb_checkpoints/estimators_for_free-checkpoint.ipynb
mari-linhares/tensorflow-workshop
apache-2.0
Running a second time Okay, the model is definitely not good... But, check OUTPUT_DIR path, you'll see that a output_dir folder was created and that there are a lot of files there that were created automatically by TensorFlow! So, most of these files are actually checkpoints, this means that if we run the experiment ...
STEPS = STEPS + 1000 learn_runner.run(generate_experiment_fn(), run_config=tf.contrib.learn.RunConfig(model_dir=OUTPUT_DIR))
code_samples/estimators-for-free/.ipynb_checkpoints/estimators_for_free-checkpoint.ipynb
mari-linhares/tensorflow-workshop
apache-2.0
Tensorboard Another thing we get for free is tensorboard. If you run: tensorboard --logdir=OUTPUT_DIR You'll see that we get the graph and some scalars, also if you use an embedding layer you'll get an embedding visualization in tensorboard as well! So, we can make small changes and we'll have an easy (and totally for...
LEARNING_RATE = 0.05 OUTPUT_DIR = 'output_dir/model2' learn_runner.run(generate_experiment_fn(), run_config=tf.contrib.learn.RunConfig(model_dir=OUTPUT_DIR))
code_samples/estimators-for-free/.ipynb_checkpoints/estimators_for_free-checkpoint.ipynb
mari-linhares/tensorflow-workshop
apache-2.0
Load the volume and look at the image (visualization requires window-leveling).
spherical_fiducials_image = sitk.ReadImage(fdata("spherical_fiducials.mha")) sitk.Show(spherical_fiducials_image, "spheres")
33_Segmentation_Thresholding_Edge_Detection.ipynb
thewtex/SimpleITK-Notebooks
apache-2.0
After looking at the image you should have identified two spheres. Now select a Region Of Interest (ROI) around the sphere which you want to analyze.
rois = {"ROI1":[range(280,320), range(65,90), range(8, 30)], "ROI2":[range(200,240), range(65,100), range(15, 40)]} mask_value = 255 def select_roi_dropdown_callback(roi_name, roi_dict): global mask, mask_ranges mask_ranges = roi_dict.get(roi_name) if mask_ranges: mask = sitk.Image(spher...
33_Segmentation_Thresholding_Edge_Detection.ipynb
thewtex/SimpleITK-Notebooks
apache-2.0
Thresholding based approach To see whether this approach is appropriate we look at the histogram of intensity values inside the ROI. We know that the spheres have higher intensity values. Ideally we would have a bimodal distribution with clear separation between the sphere and background.
intensity_values = sitk.GetArrayFromImage(spherical_fiducials_image) roi_intensity_values = intensity_values[mask_ranges[2][0]:mask_ranges[2][-1], mask_ranges[1][0]:mask_ranges[1][-1], mask_ranges[0][0]:mask_ranges[0][-1]].flatten() plt.his...
33_Segmentation_Thresholding_Edge_Detection.ipynb
thewtex/SimpleITK-Notebooks
apache-2.0
Can you identify the region of the histogram associated with the sphere? In our case it looks like we can automatically select a threshold separating the sphere from the background. We will use Otsu's method for threshold selection to segment the sphere and estimate its radius.
# Set pixels that are in [min_intensity,otsu_threshold] to inside_value, values above otsu_threshold are # set to outside_value. The sphere's have higher intensity values than the background, so they are outside. inside_value = 0 outside_value = 255 number_of_histogram_bins = 100 mask_output = True labeled_result = s...
33_Segmentation_Thresholding_Edge_Detection.ipynb
thewtex/SimpleITK-Notebooks
apache-2.0
Based on your visual inspection, did the automatic threshold correctly segment the sphere or did it over/under segment it? If automatic thresholding did not provide the desired result, you can correct it by allowing the user to modify the threshold under visual inspection. Implement this approach below.
# Your code here:
33_Segmentation_Thresholding_Edge_Detection.ipynb
thewtex/SimpleITK-Notebooks
apache-2.0
Edge detection based approach In this approach we will localize the sphere's edges in 3D using SimpleITK. We then compute the least squares sphere that optimally fits the 3D points using scipy/numpy. The mathematical formulation for this solution is described in this Insight Journal paper.
# Create a cropped version of the original image. sub_image = spherical_fiducials_image[mask_ranges[0][0]:mask_ranges[0][-1], mask_ranges[1][0]:mask_ranges[1][-1], mask_ranges[2][0]:mask_ranges[2][-1]] # Edge detection on the sub_image with ap...
33_Segmentation_Thresholding_Edge_Detection.ipynb
thewtex/SimpleITK-Notebooks
apache-2.0
Get the 3D location of the edge points and fit a sphere to them.
edge_indexes = np.where(sitk.GetArrayFromImage(edges) == 1.0) # Note the reversed order of access between SimpleITK and numpy (z,y,x) physical_points = [edges.TransformIndexToPhysicalPoint([int(x), int(y), int(z)]) \ for z,y,x in zip(edge_indexes[0], edge_indexes[1], edge_indexes[2])] # Setup and s...
33_Segmentation_Thresholding_Edge_Detection.ipynb
thewtex/SimpleITK-Notebooks
apache-2.0
As always, let's do imports and initialize a logger and a new bundle.
import phoebe from phoebe import u # units import numpy as np import matplotlib.pyplot as plt logger = phoebe.logger() b = phoebe.default_binary()
2.3/examples/animation_binary_complete.ipynb
phoebe-project/phoebe2-docs
gpl-3.0
Adding Datasets
times = np.linspace(0,1,21) b.add_dataset('lc', times=times, dataset='lc01') b.add_dataset('rv', times=times, dataset='rv01') b.add_dataset('mesh', times=times, columns=['visibilities', 'intensities@lc01', 'rvs@rv01'], dataset='mesh01')
2.3/examples/animation_binary_complete.ipynb
phoebe-project/phoebe2-docs
gpl-3.0
Plotting See the Animations Tutorial for more examples and details. Here we'll create a figure with multiple subplots. The top row will be the light curve and RV curve. The bottom three subplots will be various representations of the mesh (intensities, rvs, and visibilities). We'll do this by making separate calls to...
b['lc01@model'].plot(axpos=221) b['rv01@model'].plot(c={'primary': 'blue', 'secondary': 'red'}, linestyle='solid', axpos=222) b['mesh@model'].plot(fc='intensities@lc01', ec='None', axpos=425) b['mesh@model'].plot(fc='rvs@rv01', ec='None', axpos=427) b['mesh@model'].plot(fc='visibilities', ec='None', y='ws', axpos=224) ...
2.3/examples/animation_binary_complete.ipynb
phoebe-project/phoebe2-docs
gpl-3.0
Building the Classifier Now that we have codes for all the images, we can build a simple classifier on top of them. The codes behave just like normal input into a simple neural network. Below I'm going to have you do most of the work.
# read codes and labels from file import csv with open('labels') as f: reader = csv.reader(f, delimiter='\n') labels = np.array([each for each in reader if len(each) > 0]).squeeze() with open('codes') as f: codes = np.fromfile(f, dtype=np.float32) codes = codes.reshape((len(labels), -1))
week2/vgg_transfer_imagenet_to_flower/transfer_learning_python.ipynb
infilect/ml-course1
mit
Plot dynamics functions
if data_dim == 2: lim = 5 x = np.linspace(-lim, lim, 10) y = np.linspace(-lim, lim, 10) X, Y = np.meshgrid(x, y) xy = np.column_stack((X.ravel(), Y.ravel())) fig, axs = plt.subplots(1, num_states, figsize=(3 * num_states, 6)) for k in range(num_states): A, b = weights[k], biases[k] ...
deprecated/arhmm_example.ipynb
probml/pyprobml
mit
Sample data from the ARHMM
# Make an Autoregressive (AR) HMM true_initial_distribution = tfp.distributions.Categorical(logits=np.zeros(num_states)) true_transition_distribution = tfp.distributions.Categorical(probs=transition_matrix) true_arhmm = GaussianARHMM( num_states, transition_matrix=transition_matrix, emission_weights=weight...
deprecated/arhmm_example.ipynb
probml/pyprobml
mit
Below, we visualize each component of of the observation variable as a time series. The colors correspond to the latent state. The dotted lines represent the stationary point of the the corresponding AR state while the solid lines are the actual observations sampled from the HMM.
lim # Plot the data and the smoothed data plot_slice = (0, 200) lim = 1.05 * abs(data).max() plt.figure(figsize=(8, 6)) plt.imshow( true_states[None, :], aspect="auto", cmap=cmap, vmin=0, vmax=len(colors) - 1, extent=(0, time_bins, -lim, (data_dim) * lim), ) Ey = np.array(stationary_points)[t...
deprecated/arhmm_example.ipynb
probml/pyprobml
mit
Fit an ARHMM
# Now fit an HMM to the data key1, key2 = jr.split(jr.PRNGKey(0), 2) test_num_states = num_states initial_distribution = tfp.distributions.Categorical(logits=np.zeros(test_num_states)) transition_distribution = tfp.distributions.Categorical(logits=np.zeros((test_num_states, test_num_states))) emission_distribution = Ga...
deprecated/arhmm_example.ipynb
probml/pyprobml
mit
Implement Preprocessing Function Text to Word Ids As you did with other RNNs, you must turn the text into a number so the computer can understand it. In the function text_to_ids(), you'll turn source_text and target_text from words to ids. However, you need to add the <EOS> word id at the end of target_text. Th...
def text_to_ids(source_text, target_text, source_vocab_to_int, target_vocab_to_int): """ Convert source and target text to proper word ids :param source_text: String that contains all the source text. :param target_text: String that contains all the target text. :param source_vocab_to_int: Dictionar...
language-translation/dlnd_language_translation.ipynb
hvillanua/deep-learning
mit
Build the Neural Network You'll build the components necessary to build a Sequence-to-Sequence model by implementing the following functions below: - model_inputs - process_decoder_input - encoding_layer - decoding_layer_train - decoding_layer_infer - decoding_layer - seq2seq_model Input Implement the model_inputs() fu...
def model_inputs(): """ Create TF Placeholders for input, targets, learning rate, and lengths of source and target sequences. :return: Tuple (input, targets, learning rate, keep probability, target sequence length, max target sequence length, source sequence length) """ # TODO: Implement Functio...
language-translation/dlnd_language_translation.ipynb
hvillanua/deep-learning
mit
Process Decoder Input Implement process_decoder_input by removing the last word id from each batch in target_data and concat the GO ID to the begining of each batch.
def process_decoder_input(target_data, target_vocab_to_int, batch_size): """ Preprocess target data for encoding :param target_data: Target Placehoder :param target_vocab_to_int: Dictionary to go from the target words to an id :param batch_size: Batch Size :return: Preprocessed target data "...
language-translation/dlnd_language_translation.ipynb
hvillanua/deep-learning
mit
Encoding Implement encoding_layer() to create a Encoder RNN layer: * Embed the encoder input using tf.contrib.layers.embed_sequence * Construct a stacked tf.contrib.rnn.LSTMCell wrapped in a tf.contrib.rnn.DropoutWrapper * Pass cell and embedded input to tf.nn.dynamic_rnn()
from imp import reload reload(tests) def encoding_layer(rnn_inputs, rnn_size, num_layers, keep_prob, source_sequence_length, source_vocab_size, encoding_embedding_size): """ Create encoding layer :param rnn_inputs: Inputs for the RNN :param rnn_size: RNN Size ...
language-translation/dlnd_language_translation.ipynb
hvillanua/deep-learning
mit
Decoding - Training Create a training decoding layer: * Create a tf.contrib.seq2seq.TrainingHelper * Create a tf.contrib.seq2seq.BasicDecoder * Obtain the decoder outputs from tf.contrib.seq2seq.dynamic_decode
def decoding_layer_train(encoder_state, dec_cell, dec_embed_input, target_sequence_length, max_summary_length, output_layer, keep_prob): """ Create a decoding layer for training :param encoder_state: Encoder State :param dec_cell: Decoder RNN Cell ...
language-translation/dlnd_language_translation.ipynb
hvillanua/deep-learning
mit
Decoding - Inference Create inference decoder: * Create a tf.contrib.seq2seq.GreedyEmbeddingHelper * Create a tf.contrib.seq2seq.BasicDecoder * Obtain the decoder outputs from tf.contrib.seq2seq.dynamic_decode
def decoding_layer_infer(encoder_state, dec_cell, dec_embeddings, start_of_sequence_id, end_of_sequence_id, max_target_sequence_length, vocab_size, output_layer, batch_size, keep_prob): """ Create a decoding layer for inference :param encoder_state: Encoder ...
language-translation/dlnd_language_translation.ipynb
hvillanua/deep-learning
mit
Build the Decoding Layer Implement decoding_layer() to create a Decoder RNN layer. Embed the target sequences Construct the decoder LSTM cell (just like you constructed the encoder cell above) Create an output layer to map the outputs of the decoder to the elements of our vocabulary Use the your decoding_layer_train(e...
def decoding_layer(dec_input, encoder_state, target_sequence_length, max_target_sequence_length, rnn_size, num_layers, target_vocab_to_int, target_vocab_size, batch_size, keep_prob, decoding_embedding_size): """ Create decoding layer ...
language-translation/dlnd_language_translation.ipynb
hvillanua/deep-learning
mit
Build the Neural Network Apply the functions you implemented above to: Encode the input using your encoding_layer(rnn_inputs, rnn_size, num_layers, keep_prob, source_sequence_length, source_vocab_size, encoding_embedding_size). Process target data using your process_decoder_input(target_data, target_vocab_to_int, bat...
def seq2seq_model(input_data, target_data, keep_prob, batch_size, source_sequence_length, target_sequence_length, max_target_sentence_length, source_vocab_size, target_vocab_size, enc_embedding_size, dec_embedding_size, rnn_size, ...
language-translation/dlnd_language_translation.ipynb
hvillanua/deep-learning
mit
Neural Network Training Hyperparameters Tune the following parameters: Set epochs to the number of epochs. Set batch_size to the batch size. Set rnn_size to the size of the RNNs. Set num_layers to the number of layers. Set encoding_embedding_size to the size of the embedding for the encoder. Set decoding_embedding_siz...
# Number of Epochs epochs = 10 # Batch Size batch_size = 128 # RNN Size rnn_size = 254 # Number of Layers num_layers = 2 # Embedding Size encoding_embedding_size = 200 decoding_embedding_size = 200 # Learning Rate learning_rate = 0.01 # Dropout Keep Probability keep_probability = 0.5 display_step = 10
language-translation/dlnd_language_translation.ipynb
hvillanua/deep-learning
mit
Train Train the neural network on the preprocessed data. If you have a hard time getting a good loss, check the forums to see if anyone is having the same problem.
""" DON'T MODIFY ANYTHING IN THIS CELL """ def get_accuracy(target, logits): """ Calculate accuracy """ max_seq = max(target.shape[1], logits.shape[1]) if max_seq - target.shape[1]: target = np.pad( target, [(0,0),(0,max_seq - target.shape[1])], 'constant'...
language-translation/dlnd_language_translation.ipynb
hvillanua/deep-learning
mit
Sentence to Sequence To feed a sentence into the model for translation, you first need to preprocess it. Implement the function sentence_to_seq() to preprocess new sentences. Convert the sentence to lowercase Convert words into ids using vocab_to_int Convert words not in the vocabulary, to the <UNK> word id.
def sentence_to_seq(sentence, vocab_to_int): """ Convert a sentence to a sequence of ids :param sentence: String :param vocab_to_int: Dictionary to go from the words to an id :return: List of word ids """ # TODO: Implement Function sentence = sentence.lower() sentence_to_id = [vocab_...
language-translation/dlnd_language_translation.ipynb
hvillanua/deep-learning
mit
Turn the relative refference of the current directory, '.' into an absolute path. Then specify the file name that we're looking for. And in a while-loop look upward in an ever higher diectory in the directory tree until we found that with our file. Walking upward in the tree is done by cutting off the tail of the path ...
apth = os.path.abspath('.') fname = 'README.md' print("Starting in folder <{}>,\n to look for file <{}> ...".format(apth, fname)) print() print("I'm searching: ...") while not fname in os.listdir(apth): apth = apth.rpartition(os.sep)[0] print(apth) if fname in os.listdir(apth): print("... Yep, got'm...
exercises/Mar07/readingText.ipynb
Olsthoorn/IHE-python-course-2017
gpl-2.0
Reading the file (at once) When we know where the file is, we can open it for reading. We have to open it, which yields a reader object, by which we can read the file. reader = open(path, 'r') s = reader.read() reader.close() Problem with this, is that when we are exploring the reader, we may easily reach the end of fi...
with open(os.path.join(apth, fname), 'r') as reader: s = reader.read()
exercises/Mar07/readingText.ipynb
Olsthoorn/IHE-python-course-2017
gpl-2.0
It's the read that swallows the entire file at once and dumps its contents in the string s. Check if the reader in, indeed, closed after we finished the with block:
reader.closed
exercises/Mar07/readingText.ipynb
Olsthoorn/IHE-python-course-2017
gpl-2.0
Then show the contenct of the sring s:
print(s)
exercises/Mar07/readingText.ipynb
Olsthoorn/IHE-python-course-2017
gpl-2.0
Counting words and phrases Now that we have the entire file read into a single string, s, we can just as well analyze it a bit, by counting the number of words, letters, and the frequency of each letter. just split the sting in workds based on whitespace and count their number.
print("There are {} words in file {}".format(len(s.split(sep=' ')), fname))
exercises/Mar07/readingText.ipynb
Olsthoorn/IHE-python-course-2017
gpl-2.0
We might estimate the number of sentences by counting the number of periods '.' One way is to use the . as a separator:
nPhrases = len(s.split(sep='.')) # also works without the keyword sep print("We find {} phrases in file {}".format(nPhrases, fname))
exercises/Mar07/readingText.ipynb
Olsthoorn/IHE-python-course-2017
gpl-2.0
We could just as wel count the number of dots in s directly, using one of the string methods, in this case s.count()
print("There are {} dots in file {}".format(s.count('.'), fname))
exercises/Mar07/readingText.ipynb
Olsthoorn/IHE-python-course-2017
gpl-2.0
Counting the non-whitespace characters Now let's see how many non-whitespace characters there are in s. A coarse way to remove whitespace would be splitting s and rejoining the obtained list of words without any whitespace like so:
s1 = "".join(s.split()).lower() # also make all letters in lowerface() print(s1)
exercises/Mar07/readingText.ipynb
Olsthoorn/IHE-python-course-2017
gpl-2.0
All characters in a list If we convert a string into a list, we get the list of its individual characters.
list(s1)
exercises/Mar07/readingText.ipynb
Olsthoorn/IHE-python-course-2017
gpl-2.0