Python utils.shuffle函数代码示例

def generate_feature(in_file, dump=False, single_only=False, min_count=0):
  f = open(in_file, 'r')
  f.readline()
  training_data, tags = [], []
  total_features = {}

  for line in f.readlines():
    tokens = line.replace('\n', '').split(',')
    fs = [s for s in tokens[1:] if s.isdigit()]
    # ignore invalid data
    if len(fs) != 10:
      continue
    tags.append(tokens[0])
    features = get_feature_array(fs, single_only)
    update_total_features(total_features, features)
    training_data.append(features)

  training_data = transform_to_matrix(total_features, training_data)
  training_data = cut_off(training_data, min_count)
  shuffle(training_data, tags)
  tags = np.array(tags)
  if dump:
    np.savetxt('preprocessing/dumpX.txt', training_data, fmt='%d', delimiter=',')
    np.savetxt('preprocessing/dumpY.txt', tags[np.newaxis].T, fmt='%s', delimiter=',')
  return total_features, training_data, np.array(tags)

 def _subsample_data(self, X, Y, n=10000):
   if Y is not None:
     X, Y = shuffle(X, Y)
     return X[:n], Y[:n]
   else:
     X = shuffle(X)
     return X[:n]

def main(is_binary=True):
    train, test, word2idx = get_ptb_data()

    for t in train:
        add_idx_to_tree(t, 0)
    train = [tree2list(t, -1, is_binary) for t in train]
    if is_binary:
        train = [t for t in train if t[3][-1] >= 0] # for filtering binary labels

    for t in test:
        add_idx_to_tree(t, 0)
    test = [tree2list(t, -1, is_binary) for t in test]
    if is_binary:
        test = [t for t in test if t[3][-1] >= 0] # for filtering binary labels

    train = shuffle(train)
    train = train[:5000]
    # n_pos = sum(t[3][-1] for t in train)
    # print "n_pos train:", n_pos
    test = shuffle(test)
    test = test[:1000]
    # n_pos = sum(t[3][-1] for t in test)
    # print "n_pos test:", n_pos

    V = len(word2idx)
    print "vocab size:", V
    D = 20
    K = 2 if is_binary else 5

    model = RecursiveNN(V, D, K)
    model.fit(train)
    print "train accuracy:", model.score(train)
    print "test accuracy:", model.score(test)
    print "train f1:", model.f1_score(train)
    print "test f1:", model.f1_score(test)

def splitIntoTrainingAndValidation(A, B):
	data1 = shuffle(sourceSets[A])    # Note this is a random shuffle, that's
	data2 = shuffle(sourceSets[B])    #                                   why we need many iterations
	freqM = np.minimum(freqs[A], freqs[B])
	freq1tr = np.round(freqM * 0.8)        # Randomly selected 80% for the training set,
	freq1va = freqM - freq1tr              # and the remaining 20% for the validation set
	freq2tr = np.copy(freq1tr)
	freq2va = np.copy(freq1va)
	trainingSetSize = int(sum(freq1tr))  # 1/2 size actually
	validatnSetSize = int(sum(freq1va))
	testSet1size = len(data1) - trainingSetSize - validatnSetSize
	testSet2size = len(data2) - trainingSetSize - validatnSetSize
	X  = np.zeros((trainingSetSize*2,         numFeatures))
	Xv = np.zeros((validatnSetSize*2,         numFeatures))
	Xt = np.zeros((testSet1size+testSet2size, numFeatures))
	y  = np.ravel([([0]*trainingSetSize) + ([1]*trainingSetSize)])
	yv = np.ravel([([0]*validatnSetSize) + ([1]*validatnSetSize)])
	yt = np.ravel([([0]*testSet1size)    + ([1]*testSet2size)])
	trnIdx = vldIdx = tstIdx = 0
	for item in data1:
		year = item[0]
		if   freq1tr[year] > 0:   X[trnIdx], trnIdx, freq1tr[year]  =  item[1:],  trnIdx+1,  freq1tr[year]-1
		elif freq1va[year] > 0:  Xv[vldIdx], vldIdx, freq1va[year]  =  item[1:],  vldIdx+1,  freq1va[year]-1
		else:                    Xt[tstIdx], tstIdx                 =  item[1:],  tstIdx+1
	assert trnIdx==trainingSetSize   and vldIdx==validatnSetSize   and tstIdx==testSet1size
	for item in data2:
		year = item[0]
		if   freq2tr[year] > 0:   X[trnIdx], trnIdx, freq2tr[year]  =  item[1:],  trnIdx+1,  freq2tr[year]-1
		elif freq2va[year] > 0:  Xv[vldIdx], vldIdx, freq2va[year]  =  item[1:],  vldIdx+1,  freq2va[year]-1
		else:                    Xt[tstIdx], tstIdx                 =  item[1:],  tstIdx+1
	assert trnIdx==trainingSetSize*2 and vldIdx==validatnSetSize*2 and tstIdx==testSet1size+testSet2size
	X, y = shuffle(X, y)   # Just in case... perhaps no reason to shuffle again here?
	fs = SelectKBest(f_classif, k = numFeatures)   # TODO: try other feature selection methods?
	fs.fit(np.concatenate((X, Xv)), np.concatenate((y, yv)))
	return X, y, Xv, yv, Xt, yt, testSet1size, testSet2size, fs.scores_

    def compute_distances_and_pairs(self, pdb_file, nr_contacts=None, nr_noncontacts=None):
        #distance and contacts
        self.features['pair']['Cbdist'] = pdb.distance_map(pdb_file, self.L)

        #mask positions that have too many gaps
        gap_freq = 1 - (self.Ni / self.neff)
        highly_gapped_pos = np.where(gap_freq > self.max_gap_percentage)[0]
        self.features['pair']['Cbdist'][:,highly_gapped_pos] = np.nan
        self.features['pair']['Cbdist'][highly_gapped_pos, :] = np.nan

        #if there are unresolved residues, there will be nan in the distance_map
        with np.errstate(invalid='ignore'):
            self.features['pair']['contact'] = (self.features['pair']['Cbdist'] <= self.contact_threshold) * 1
            self.features['pair']['nocontact'] = (self.features['pair']['Cbdist'] > self.non_contact_threshold) * 1

        indices_contact = np.where(np.triu(self.features['pair']['contact'], k=self.seq_separation))
        indices_contact = tuple(shuffle(indices_contact[0],indices_contact[1], random_state=0))
        if nr_contacts:
            indices_contact = indices_contact[0][:nr_contacts], indices_contact[1][:nr_contacts]

        indices_nocontact = np.where(np.triu(self.features['pair']['nocontact'], k=self.seq_separation))
        indices_nocontact = tuple(shuffle(indices_nocontact[0],indices_nocontact[1], random_state=0))
        if nr_noncontacts:
            indices_nocontact = indices_nocontact[0][:nr_noncontacts], indices_nocontact[1][:nr_noncontacts]


        #update indices of i<j for only relevant pairs
        self.ij_ind_upper = np.array(list(indices_contact[0]) + list(indices_nocontact[0])), np.array(list(indices_contact[1]) + list(indices_nocontact[1]))

def get_aa_cross_val(L, X, Y, AA, tsize=None, rstate=-1):
    """Get test data from dataset"""
    test_position = []
    aa_y = np.zeros(Y.shape)
    for i in xrange(len(Y)):
        if L[i][-1] == AA:
            aa_y[i] = 1
            test_position.append(i)

    if tsize:
        t_len = int(tsize * len(Y))
        # positions that are 0 without being the one for AA
        zero_pos = np.where(np.logical_and(Y == 0, aa_y == 0))[0]
        clen = t_len - len(test_position)
        if clen > 0:
            random_zero_pos = np.random.choice(zero_pos, clen, replace=False)
            test_position.extend(random_zero_pos)

    test_position = np.random.permutation(test_position)
    mask = np.ones(Y.shape, dtype=bool)
    mask[test_position] = False
    train_position = np.array(range(len(mask)))[mask]

    if rstate > 0:
        return shuffle(train_position, random_state=rstate), shuffle(test_position, random_state=rstate)
    # in this case, suppose we want only the train and test index
    else:
        return train_position, test_position

def generator3(samples, batch_size=32):
    num_samples = len(samples)
    
    while 1: # Loop forever so the generator never terminates
        shuffle(samples)
        for offset in range(0, num_samples, batch_size):
            batch_samples = samples[offset:offset+batch_size]

            car_images = []
            steering_angles = []
            for batch_sample in batch_samples:
                img_center = cv2.imread(path+batch_sample[0].split('\\')[-1])
                img_left   = cv2.imread(path+batch_sample[1].split('\\')[-1])
                img_right  = cv2.imread(path+batch_sample[2].split('\\')[-1])
                
                correction = 0.3 # this is a parameter to tune
                steering_center = float(batch_sample[3])
                steering_left   = steering_center + correction
                steering_right  = steering_center - correction
                
                # add images and angles to data set
                car_images.extend([img_center, img_left, img_right])
                steering_angles.extend([steering_center, steering_left, steering_right])
                
            # trim image to only see section with road
            X_train = np.array(car_images)
            y_train = np.array(steering_angles)
            yield shuffle(X_train, y_train)

def import_images():
	#IMPLEMENT TIMER CUTOFF FR+OR IF FEAT EXT TAKES TOO LONG
	d_feats = {'orb': []}
	c_feats = {'orb': []}
	(cat_paths, dog_paths) = get_filenames(TRAINING_FOLDER)
	cat_train_pts = []
	dog_train_pts = []
	for image_fn in shuffle(dog_paths, n_samples = 400, random_state=0):
		odesc_pts = extract_desc_pts(image_fn)
		try:
			for pt in odesc_pts:
				d_feats['orb'].append(pt)
		except TypeError:
			print image_fn
			continue
	for image_fn in shuffle(cat_paths, n_samples = 400, random_state=0):
		odesc_pts = extract_desc_pts(image_fn)
		try:
			for pt in odesc_pts:
				c_feats['orb'].append(pt)
		except TypeError:
			print image_fn
			continue
	cat_k_means = KMeans(n_jobs=-1, n_clusters=200)
	cat_k_means.fit(c_feats['orb'])
	print 'dog calc'
	dog_k_means = KMeans(n_jobs=-1, n_clusters=200)
	dog_k_means.fit(d_feats['orb'])
	print 'saving....'
	with open('/home/max/CVD/d_o200c200s400.pickle', 'wb') as handle:
		pickle.dump(dog_k_means.cluster_centers_, handle)
	with open('/home/max/CVD/c_o200c200s400.pickle', 'wb') as handle:
		pickle.dump(cat_k_means.cluster_centers_, handle)
	return '\n\n\n DONE   '	

def generate_training_data(image_paths, angles, batch_size=128, validation_flag=False):
    '''
    method for the model training data generator to load, process, and distort images, then yield them to the
    model. if 'validation_flag' is true the image is not distorted. also flips images with turning angle magnitudes of greater than 0.33, as to give more weight to them and mitigate bias toward low and zero turning angles
    '''
    image_paths, angles = shuffle(image_paths, angles)
    X,y = ([],[])
    while True:       
        for i in range(len(angles)):
            img = cv2.imread(image_paths[i])
            angle = angles[i]
            img = preprocess_image(img)
            if not validation_flag:
                img, angle = random_distort(img, angle)
            X.append(img)
            y.append(angle)
            if len(X) == batch_size:
                yield (np.array(X), np.array(y))
                X, y = ([],[])
                image_paths, angles = shuffle(image_paths, angles)
            # flip horizontally and invert steer angle, if magnitude is > 0.33
            if abs(angle) > 0.33:
                img = cv2.flip(img, 1)
                angle *= -1
                X.append(img)
                y.append(angle)
                if len(X) == batch_size:
                    yield (np.array(X), np.array(y))
                    X, y = ([],[])
                    image_paths, angles = shuffle(image_paths, angles)

def splitIntoTrainingValidation(A, B):  # TODO: 3rd parameter: the desired value of (validatSet1size + validatSet2size)
	data1 = shuffle(sourceSets[A])    # Note this is a random shuffle, that's
	data2 = shuffle(sourceSets[B])    #                                   why we need many iterations
	freq1 = np.minimum(freqs[A], freqs[B])
	if sum(freq1) > maxTrainSetSz:  freq1 = np.round(freq1 * (maxTrainSetSz * 1.0 / sum(freq1)))
	trainingSetSize = int(sum(freq1))  # Half size actually.  Approximately <= maxTrainSetSz
	validatSet1size = len(data1) - trainingSetSize
	validatSet2size = len(data2) - trainingSetSize
	X  = np.zeros((trainingSetSize*2,               numFeatures))
	Xv = np.zeros((validatSet1size+validatSet2size, numFeatures))
	y  = np.ravel([([0]*trainingSetSize) + ([1]*trainingSetSize)])
	yv = np.ravel([([0]*validatSet1size) + ([1]*validatSet2size)])
	freq2  = np.copy(freq1)
	trnIdx = valIdx = 0
	for item in data1:
		year = item[0]
		if freq1[year] > 0:
					freq1[year]-=1
					X[trnIdx] = item[1:]
					trnIdx+=1
		else:
			  Xv[valIdx] = item[1:]
			  valIdx += 1
	assert trnIdx==trainingSetSize and valIdx==validatSet1size
	for item in data2:
		year = item[0]
		if freq2[year] > 0:
					freq2[year]-=1
					X[trnIdx] = item[1:]
					trnIdx+=1
		else:
			  Xv[valIdx] = item[1:]
			  valIdx += 1
	assert trnIdx==trainingSetSize*2 and valIdx==validatSet1size+validatSet2size
	return X, y, Xv, yv, validatSet1size, validatSet2size

def cluster(m, n_colors=32):
    from sklearn.utils import shuffle
    from sklearn.cluster import KMeans
    from sklearn.metrics import pairwise_distances_argmin

    def recreate_image(codebook, labels, w, h):
        """Recreate the (compressed) image from the code book & labels"""
        d = codebook.shape[1]
        image = np.zeros((w, h, d))
        label_idx = 0
        for i in range(w):
            for j in range(h):
                image[i][j] = codebook[labels[label_idx]]
                label_idx += 1
        return image

    # Load Image and transform to a 2D numpy array.
    w, h, d = original_shape = tuple(m.shape)
    image_array = np.reshape(m, (w * h, d))
    image_array_sample = shuffle(image_array, random_state=0)[:1000]
    kmeans = KMeans(n_clusters=n_colors).fit(image_array_sample)

    codebook_random = shuffle(image_array, random_state=0)[:n_colors + 1]
    labels_random = pairwise_distances_argmin(codebook_random, image_array, axis=0)

    return recreate_image(codebook_random, labels_random, w, h)

def main():
    train, test, word2idx = get_ptb_data()

    for t in train:
        add_idx_to_tree(t, 0)
    train = [tree2list(t, -1, True) for t in train]
    train = [t for t in train if t[3][-1] >= 0] # for filtering binary labels

    for t in test:
        add_idx_to_tree(t, 0)
    test = [tree2list(t, -1, True) for t in test]
    test = [t for t in test if t[3][-1] >= 0] # for filtering binary labels

    train = shuffle(train)
    train = train[:1000]
    # n_pos = sum(t[3][-1] for t in train)
    # print "n_pos train:", n_pos
    test = shuffle(test)
    test = test[:100]
    # n_pos = sum(t[3][-1] for t in test)
    # print "n_pos test:", n_pos

    V = len(word2idx)
    print "vocab size:", V
    D = 80
    K = 5

    model = RecursiveNN(V, D, K)
    model.fit(train, epochs=3, activation=T.nnet.relu)
    print "train accuracy:", model.score(train)
    print "test accuracy:", model.score(test)
    print "train f1:", model.f1_score(train)
    print "test f1:", model.f1_score(test)

def process_data():
  global num_classes, num_train, num_test

  X_train , Y_train = load_data('Train')
  X_test , Y_test = load_data('Test')
  X_train = X_train.astype(np.float64)
  X_test = X_test.astype(np.float64)
  num_train = X_train.shape[0]
  num_test = X_test.shape[0]

  mean_image = np.mean(X_train,axis=0)
  X_train -= mean_image
  X_test -= mean_image

  X_train = X_train.reshape(-1, 1, img_dim, img_dim)
  Y_train -= 1
  X_train , Y_train = shuffle(X_train, Y_train)

  X_test = X_test.reshape(-1, 1, img_dim, img_dim)
  Y_test -= 1
  X_test , Y_test = shuffle(X_test, Y_test)

  print 'Training X shape :- ', X_train.shape
  print 'Training Y shape :- ', Y_train.shape
  print 'Testing X shape :- ', X_test.shape
  print 'Testing Y shape :- ', Y_test.shape

  return X_train, Y_train, X_test, Y_test

 def frames2batch(k = 12,batch_size = 1024, is_calib = False):
     pos = util.get_files(rootdir = 'F:\\train_data\\pos\\')
     neg = util.get_files(rootdir = 'F:\\train_data\\neg\\')
     pos = shuffle(pos)
     neg = shuffle(neg)
     total = pos + neg
     total  = shuffle(total)
     batch = []
     c = 0
     bpath = 'F:\\train_data\\batch\\'
     for item_path in total:
         
         frame = fr.get_frame(item_path)
         frame_r = fr.resize_frame(frame,(k,k))
         if frame_r == None:
             continue
         vec = fr.frame_to_vect(frame_r)
         label = 1 if item_path.split('\\')[-1].find('pos') > 0 else 0
         print(item_path,label)
         batch.append((vec,label))
         if len(batch) > 0 and len(batch) % batch_size == 0:
             batch = sp.array(batch)
             sp.savez(bpath + str(c) + '_' + str(k) + ('_' if not is_calib else '_calib-')  + 'net',batch)
             batch = []
             
             c += 1
     if len(batch) > 0 and len(batch) % batch_size == 0:
         batch = sp.array(batch)
         sp.savez(bpath + str(c) + '_' + str(k) + ('_' if not is_calib else '_calib')  + '-net',batch)
         batch = []
         c += 1

def getMNIST():
    # data shape: train (50000, 784), test (10000, 784)
    # already scaled from 0..1 and converted to float32
    datadir = '../large_files/'
    if not os.path.exists(datadir):
        datadir = ''

    input_file = "%smnist.pkl.gz" % datadir
    if not os.path.exists(input_file):
        url = 'http://www.iro.umontreal.ca/~lisa/deep/data/mnist/mnist.pkl.gz'
        with open(input_file, "wb") as out:
            f = urllib2.urlopen(url)
            out.write(f.read())
            out.flush()

    with gzip.open(input_file) as f:
        train, valid, test = cPickle.load(f)

    Xtrain, Ytrain = train
    Xvalid, Yvalid = valid
    Xtest, Ytest = test

    Ytrain_ind = y2indicator(Ytrain)
    Ytest_ind = y2indicator(Ytest)

    Xtrain, Ytrain = shuffle(Xtrain, Ytrain)
    Xtest, Ytest = shuffle(Xtest, Ytest)

    # try to take a smaller sample
    Xtrain = Xtrain[0:30000]
    Ytrain = Ytrain[0:30000]
    Xtest = Xtest[0:1000]
    Ytest = Ytest[0:1000]

    return Xtrain.reshape(len(Xtrain), 1, 28, 28), Ytrain, Ytrain_ind, Xtest.reshape(len(Xtest), 1, 28, 28), Ytest, Ytest_ind