def build_classifier(train_data_x_in, train_data_y, classifier_in="svc_basic"):
print "Attempting to build classifier."
train_data_x = train_data_x_in
transformer = ""
# classifier = grid_search.GridSearchCV(svm.SVC(), parameters).fit(train_data_x, train_data_y)
if classifier_in == "svc_basic":
classifier = svm.SVC()
print "Selection was basic svm.SVC."
elif classifier_in == "svc_extensive":
classifier = svm.SVC(kernel="linear", C=0.025, gamma=0.01)
print "Selection was extensive svm.SVC, with linear kernel, C==0.025 and gamma==0.01."
elif classifier_in == "kneighbors_basic":
transformer = RandomizedPCA(n_components=2000)
train_data_x = transformer.fit_transform(train_data_x)
classifier = KNeighborsClassifier()
print "Selection was KNeighbors basic, using RandomizedPCA to transform data first. n_components==2000."
elif classifier_in == "bagging_basic":
classifier = BaggingClassifier(KNeighborsClassifier(), max_samples=0.5, max_features=0.5)
print "Selection was Bagging basic, with max_samples==0.5 and max_features==0.5."
elif classifier_in == "spectral_basic":
transformer = SpectralEmbedding(n_components=2000)
train_data_x = transformer.fit_transform(train_data_x)
classifier = KNeighborsClassifier()
print "Selection was Spectral basic, using svm.SVC with Spectral data fitting. n_components==2000."
# default to SVC in case of any sort of parsing error.
else:
print "Error in selecting classifier class. Reverting to SVC."
classifier = svm.SVC()
classifier.fit(train_data_x, train_data_y)
print "Doing classifier estimation."
return classifier, train_data_x, transformer
def reduce_features(features,
var_explained=0.9,
n_components=0,
verbose=False):
"""
Performs feature reduction using PCA. Automatically selects nr. components
for explaining min_var_explained variance.
:param features: Features.
:param var_explained: Minimal variance explained.
:param n_components: Nr. of components.
:param exclude_columns: Columns to exclude.
:param verbose: Verbosity.
:return: Reduced feature set.
"""
if n_components == 0:
# Run full PCA to estimate nr. components for explaining given
# percentage of variance.
estimator = RandomizedPCA()
estimator.fit_transform(features)
variance = 0.0
for i in range(len(estimator.explained_variance_ratio_)):
variance += estimator.explained_variance_ratio_[i]
if variance > var_explained:
n_components = i + 1
if verbose:
print('{} % of variance explained using {} components'.
format(var_explained, n_components))
break
# Re-run PCA with only estimated nr. components
estimator = RandomizedPCA(n_components=n_components)
features = estimator.fit_transform(features)
return features
def test_feature_union_weights():
# test feature union with transformer weights
iris = load_iris()
X = iris.data
y = iris.target
pca = RandomizedPCA(n_components=2, random_state=0)
select = SelectKBest(k=1)
# test using fit followed by transform
fs = FeatureUnion([("pca", pca), ("select", select)],
transformer_weights={"pca": 10})
fs.fit(X, y)
X_transformed = fs.transform(X)
# test using fit_transform
fs = FeatureUnion([("pca", pca), ("select", select)],
transformer_weights={"pca": 10})
X_fit_transformed = fs.fit_transform(X, y)
# test it works with transformers missing fit_transform
fs = FeatureUnion([("mock", TransfT()), ("pca", pca), ("select", select)],
transformer_weights={"mock": 10})
X_fit_transformed_wo_method = fs.fit_transform(X, y)
# check against expected result
# We use a different pca object to control the random_state stream
assert_array_almost_equal(X_transformed[:, :-1], 10 * pca.fit_transform(X))
assert_array_equal(X_transformed[:, -1],
select.fit_transform(X, y).ravel())
assert_array_almost_equal(X_fit_transformed[:, :-1],
10 * pca.fit_transform(X))
assert_array_equal(X_fit_transformed[:, -1],
select.fit_transform(X, y).ravel())
assert_equal(X_fit_transformed_wo_method.shape, (X.shape[0], 7))
def pca(imageData=[]):
labels = ["shoe", "shirt"]
is_train = np.random.uniform(0, 1, len(imageData)) <= 0.7
y = np.where(np.array(labels) == "shirt", 1, 0)
train_x, train_y = imageData[is_train], imageData[is_train]
test_x, test_y = imageData[is_train == False], y[is_train == False]
pca = RandomizedPCA(n_components=2)
X = pca.fit_transform(imageData)
df = pd.DataFrame({
"x": X[:, 0],
"y": X[:, 1],
"label": np.where(y == 1, "shoe", "shirt")
})
colors = ["red", "yellow"]
for label, color in zip(df['label'].unique(), colors):
mask = df['label'] == label
pl.scatter(df[mask]['x'], df[mask]['y'], c=color, label=label)
pl.legend()
pl.show()
pca2 = RandomizedPCA(n_components=5)
train_x = pca2.fit_transform(train_x)
test_x = pca2.transform(test_x)
print train_x[:5]
knn = KNeighborsClassifier()
knn.fit(train_x, train_y)
return 0
def reduce_features(features, var_explained=0.9, n_components=0, verbose=False):
"""
Performs feature reduction using PCA. Automatically selects nr. components
for explaining min_var_explained variance.
:param features: Features.
:param var_explained: Minimal variance explained.
:param n_components: Nr. of components.
:param exclude_columns: Columns to exclude.
:param verbose: Verbosity.
:return: Reduced feature set.
"""
if n_components == 0:
# Run full PCA to estimate nr. components for explaining given
# percentage of variance.
estimator = RandomizedPCA()
estimator.fit_transform(features)
variance = 0.0
for i in range(len(estimator.explained_variance_ratio_)):
variance += estimator.explained_variance_ratio_[i]
if variance > var_explained:
n_components = i + 1
if verbose:
print('{} % of variance explained using {} components'.format(var_explained, n_components))
break
# Re-run PCA with only estimated nr. components
estimator = RandomizedPCA(n_components=n_components)
features = estimator.fit_transform(features)
return features
def test_feature_union_weights():
# test feature union with transformer weights
iris = load_iris()
X = iris.data
y = iris.target
pca = RandomizedPCA(n_components=2, random_state=0)
select = SelectKBest(k=1)
# test using fit followed by transform
fs = FeatureUnion([("pca", pca), ("select", select)],
transformer_weights={"pca": 10})
fs.fit(X, y)
X_transformed = fs.transform(X)
# test using fit_transform
fs = FeatureUnion([("pca", pca), ("select", select)],
transformer_weights={"pca": 10})
X_fit_transformed = fs.fit_transform(X, y)
# test it works with transformers missing fit_transform
fs = FeatureUnion([("mock", TransfT()), ("pca", pca), ("select", select)],
transformer_weights={"mock": 10})
X_fit_transformed_wo_method = fs.fit_transform(X, y)
# check against expected result
# We use a different pca object to control the random_state stream
assert_array_almost_equal(X_transformed[:, :-1], 10 * pca.fit_transform(X))
assert_array_equal(X_transformed[:, -1],
select.fit_transform(X, y).ravel())
assert_array_almost_equal(X_fit_transformed[:, :-1],
10 * pca.fit_transform(X))
assert_array_equal(X_fit_transformed[:, -1],
select.fit_transform(X, y).ravel())
assert_equal(X_fit_transformed_wo_method.shape, (X.shape[0], 7))
def pcaAndPlot(X, x_to_centroids, centroids, no_dims = 2):
pca = RandomizedPCA(n_components=no_dims)
x_trans = pca.fit_transform(X)
x_sizes = np.full((x_trans.shape[0]), 30, dtype=np.int)
plt.scatter(x_trans[:, 0], x_trans[:, 1], s=x_sizes, c=x_to_centroids)
centroids_trans = pca.fit_transform(centroids)
centroids_col = np.arange(centroids.shape[0])
centroids_sizes = np.full((centroids.shape[0]), 70, dtype=np.int)
plt.scatter(centroids_trans[:, 0], centroids_trans[:, 1], s=centroids_sizes, c=centroids_col)
plt.show()
def principal_component_analysis(x):
sizes = np.shape(x)
cols = sizes[1]
# Obtain the Principal Components, which are ordered by eigenvalues
principal_components = RandomizedPCA(n_components=cols)
principal_components.fit_transform(x)
eigenvalues = principal_components.explained_variance_
# Maximum eigenvalues reflect importance of each feature
feature_order = np.argsort(eigenvalues)[::-1][:cols]
return feature_order
def read_data_sets():
class DataSets(object):
pass
NUM_CLASSES = 7
start = time.time()
data_sets = DataSets()
# Load the training data
mat_contents = sio.loadmat('labeled_images.mat')
train_labels = mat_contents['tr_labels']
train_identities = mat_contents['tr_identity']
train_images = mat_contents['tr_images']
# Load the test data
mat_contents = sio.loadmat('public_test_images.mat')
test_images = mat_contents['public_test_images']
test_set_length = len(test_images[0][0])
# Flatten images
test_images = flattenImages(test_images)
train_images = flattenImages(train_images)
# Split train into validation set of size ~ test_set_length
train_images, train_labels, validation_images, validation_labels = splitSet(
train_images,
train_labels,
train_identities,
test_set_length)
# Convert labels to one hot vectors
train_labels = convertToOneHot(train_labels, NUM_CLASSES)
validation_labels = convertToOneHot(validation_labels, NUM_CLASSES)
# Normalize the images
sd = np.sqrt(np.var(train_images) + 0.01)
train_images = (train_images - np.mean(train_images)) / sd
sd = np.sqrt(np.var(validation_images) + 0.01)
validation_images = (validation_images - np.mean(validation_images)) / sd
pca = RandomizedPCA(n_components=15)
train_images = pca.fit_transform(train_images)
validation_images = pca.fit_transform(validation_images)
# Setup the matrixes into an accessible data set class
data_sets.train_set = DataSet(train_images, train_labels)
data_sets.validation_set = DataSet(validation_images, validation_labels)
data_sets.test_set = DataSet(test_images, np.zeros((len(test_images), NUM_CLASSES)))
print('Finished setting up data! Took {} seconds'.format(time.time() - start))
return data_sets
def get_features_from_images_PCA(img_dir,data_set):
"""
Takes in a directory and gets all the images from
it and extracts the pixel values, flattens the matrix
into an array and performs principle component analysis
to get representative subset of features from the pixel
values of the image.
"""
print "\nExtracting features from given images..."
img_names = [f for f in os.listdir(img_dir)]
images = [img_dir+ f for f in os.listdir(img_dir)]
#print images
print "\nConverting images to vectors"
data = []
for image in images:
# print image
img = img_to_matrix(image)
img = flatten_image(img)
data.append(img)
print "Converting image data to numpy array"
time.sleep(5)
data = np.array(data)
print "Finished Conversion"
time.sleep(5)
print "\nPerforming PCA to get reqd features"
features = []
pca = RandomizedPCA(n_components=14)
for i in xrange(len(data)/100):
if features == []:
split = data[0:100]
features = pca.fit_transform(split)
else:
split = data[100*i:100*(i+1)]
features = np.concatenate((features,pca.fit_transform(split)),axis=0)
print "Writing feature data to file"
f = open(data_set+"_extracted_features.txt","w")
for i in xrange(len(img_names)):
s = str(img_names[i])
for value in features[i]:
s += " "+str(value)
s += "\n"
f.write(s)
f.close()
print "Write completed"
def pcaAndPlot(X, x_to_centroids, centroids, no_dims=2):
pca = RandomizedPCA(n_components=no_dims)
x_trans = pca.fit_transform(X)
x_sizes = np.full((x_trans.shape[0]), 30, dtype=np.int)
plt.scatter(x_trans[:, 0], x_trans[:, 1], s=x_sizes, c=x_to_centroids)
centroids_trans = pca.fit_transform(centroids)
centroids_col = np.arange(centroids.shape[0])
centroids_sizes = np.full((centroids.shape[0]), 70, dtype=np.int)
plt.scatter(centroids_trans[:, 0],
centroids_trans[:, 1],
s=centroids_sizes,
c=centroids_col)
plt.show()
def main():
ap = argparse.ArgumentParser()
ap.add_argument("-i", "--image", required = True, help = "Path to the image")
args = vars(ap.parse_args())
image = cv2.imread(args["image"])
rects, img = detect(image)
cropped = []
for idx, (x1, y1, x2, y2) in enumerate(rects):
crop_img = image[y1:y1 + (y2 - y1), x1:x1 + (x2 - x1)]
crop_img = cv2.resize(crop_img, (100,100), interpolation = cv2.INTER_AREA)
cv2.imshow("image" + str(idx), crop_img)
new_img = crop_img.reshape(crop_img.shape[0] * crop_img.shape[1], 3)
cropped.append(new_img.flatten())
# reduce feature size
cropped_pca = []
pca = RandomizedPCA(n_components=100)
cropped_pca = pca.fit_transform(cropped)
# training (hardcoded for now)
clf = SVC(probability=True)
train = cropped_pca[:7]
test = cropped_pca[7:13]
# clf.fit([[0,0],[1,1]], [1, 2])
clf.fit(train, [1,2,2,1,2,1,1])
for item in test:
print clf.predict_proba(item)
print clf.predict(item)
cv2.waitKey(0)
def _prepare_pca(self, data, max_n_components):
""" Helper Function """
from sklearn.decomposition import RandomizedPCA
# sklearn < 0.11 does not support random_state argument
kwargs = {'n_components': max_n_components, 'whiten': False}
aspec = inspect.getargspec(RandomizedPCA.__init__)
if 'random_state' not in aspec.args:
warnings.warn('RandomizedPCA does not support random_state '
'argument. Use scikit-learn to version 0.11 '
'or newer to get reproducible results.')
else:
kwargs['random_state'] = 0
pca = RandomizedPCA(**kwargs)
pca_data = pca.fit_transform(data.T)
if self._explained_var > 1.0:
if self.n_components is not None: # normal n case
self._comp_idx = np.arange(self.n_components)
to_ica = pca_data[:, self._comp_idx]
else: # None case
to_ica = pca_data
self.n_components = pca_data.shape[1]
self._comp_idx = np.arange(self.n_components)
else: # float case
expl_var = pca.explained_variance_ratio_
self._comp_idx = (np.where(expl_var.cumsum() <
self._explained_var)[0])
to_ica = pca_data[:, self._comp_idx]
self.n_components = len(self._comp_idx)
return to_ica, pca
def detect(self, imageURLs, params):
array = []
for param in params:
img = self.img_to_matrix(param['imageURL'])
data = self.flatten_image(img)
array.append(data)
array = np.array(array)
pca = RandomizedPCA(n_components=5)
n_data = pca.fit_transform(array)
clf = joblib.load('src/resource/models/model.pkl')
result = clf.predict(n_data).tolist()
for param, r in zip(params, result):
raw_img = urllib2.urlopen(param['imageURL']).read()
if r == 1:
cntr = len([i for i in os.listdir("test/images/rain/") if 'rain' in i]) + 1
path = "static/images/rain_" + str(cntr) + '.jpg'
f = open(path, 'wb')
f.write(raw_img)
f.close()
# イベント情報作成
when = {'type': 'timestamp', 'time':param['time']}
where = { "type": "Point", "coordinates": [param['longitude'], param['latitude']]}
what = {'topic': {'value':u'雨'}, 'tweet': param['value']}
who = [{"type": "url", "value": param['imageURL']},
{"value": "evwh <*****@*****.**>", "type": "author"}]
event = {'observation':{'what': what, 'when': when, 'where': where, 'who': who}}
self.connection['event']['TwitterImageRainSensor'].insert(event)
def rpca(numpy_file='../data/Paintings/two_class/Paintings_train.csv'):
""" Performs randomized PCA on given numpy file.
Given a numpy file of n-rows and n-cols, where the last column is
the label and rest are features,n-rows are the samples.
:type numpy_file: string
:param numpy_file: The file name of numpy file to be analyzed.
"""
import numpy as np
import matplotlib.pyplot as pl
import pandas as pd
from sklearn.decomposition import RandomizedPCA
all_data = np.loadtxt(numpy_file,delimiter=',')
data = all_data[:,:-1]
y = all_data[:,-1]
pca = RandomizedPCA(n_components=2)
X = pca.fit_transform(data)
df = pd.DataFrame({"x": X[:, 0], "y": X[:, 1],\
"label":np.where(y==1, "realism", "abstract")})
colors = ["red", "yellow"]
for label, color in zip(df['label'].unique(), colors):
mask = df['label']==label
pl.scatter(df[mask]['x'], df[mask]['y'], c=color, label=label)
pl.legend()
pl.title('Randomized PCA analysis')
pl.show()
def main():
img_dir = 'images/'
images = [img_dir + f for f in os.listdir(img_dir)]
labels = [f.split('/')[-1].split('_')[0] for f in images]
label2ids = {v: i for i, v in enumerate(sorted(set(labels),
key=labels.index))}
y = np.array([label2ids[l] for l in labels])
data = []
for image_file in images:
img = img_to_matrix(image_file)
img = flatten_image(img)
data.append(img)
data = np.array(data)
# training samples
is_train = np.random.uniform(0, 1, len(data)) <= 0.7
train_X, train_y = data[is_train], y[is_train]
# training a classifier
pca = RandomizedPCA(n_components=5)
train_X = pca.fit_transform(train_X)
multi_svm = OneVsRestClassifier(LinearSVC())
multi_svm.fit(train_X, train_y)
# evaluating the model
test_X, test_y = data[is_train == False], y[is_train == False]
test_X = pca.transform(test_X)
print pd.crosstab(test_y, multi_svm.predict(test_X),
rownames=['Actual'], colnames=['Predicted'])
def rpca(numpy_file='../data/Paintings/two_class/Paintings_train.csv'):
""" Performs randomized PCA on given numpy file.
Given a numpy file of n-rows and n-cols, where the last column is
the label and rest are features,n-rows are the samples.
:type numpy_file: string
:param numpy_file: The file name of numpy file to be analyzed.
"""
import numpy as np
import matplotlib.pyplot as pl
import pandas as pd
from sklearn.decomposition import RandomizedPCA
all_data = np.loadtxt(numpy_file, delimiter=',')
data = all_data[:, :-1]
y = all_data[:, -1]
pca = RandomizedPCA(n_components=2)
X = pca.fit_transform(data)
df = pd.DataFrame({"x": X[:, 0], "y": X[:, 1],\
"label":np.where(y==1, "realism", "abstract")})
colors = ["red", "yellow"]
for label, color in zip(df['label'].unique(), colors):
mask = df['label'] == label
pl.scatter(df[mask]['x'], df[mask]['y'], c=color, label=label)
pl.legend()
pl.title('Randomized PCA analysis')
pl.show()
def make_pca_datapoints(terms_map, stopwords, clusters):
new_terms_map = {}
raw_data = []
target = []
for line in open(tweets_file):
tokens = line.split()
terms = [terms_map[int(term)] for term in tokens[3].split(',') if terms_map[int(term)] not in stopwords]
for term in terms:
if not term in new_terms_map:
new_terms_map[term] = len(new_terms_map)
new_term_ids = [new_terms_map[term] for term in terms]
tags = [terms_map[int(term)] for term in tokens[4].split(',')]
raw_data.append(new_term_ids)
target.append(tags)
data = lil_matrix( (len(raw_data), len(new_terms_map)) )
count = 0
for cur_vector in raw_data:
for point in cur_vector:
data[(count, point)] += 1
count += 1
pca = RandomizedPCA (n_components=100)
transformed_data = pca.fit_transform(data)
xs = []
ys = []
count = 0
for datum in transformed_data:
for tag in target[count]:
if (len(tag) > 1) and tag[1:] in clusters:
xs.append(datum)
ys.append(clusters[tag[1:]])
count += 1
del transformed_data
return xs, ys
def do_pca(corr_matrix: _nested_ndarray, num_dim: int,
min_var_explanation: float =0.7) -> _nested_ndarray:
'''
This method performs PCA on a self-correlation matrix, reducing the number of columns to `num_dim`.
If such analysis does not sufficiently explain the underlying variance in the data, an exception is
thrown.
Args:
* `corr_matrix` - a square matrix of correlations
* `num_dim` - the number of dimensions to which the data should be reduced
* `min_var_explanation` - the minimum fraction of the underlying data variance that should be explained
Returns:
> A matrix of the PCA result on `corr_matrix`.
'''
num_dim = int(num_dim)
pca = PCA(n_components=num_dim, random_state=0)
pca_result = pca.fit_transform(corr_matrix)
var_ratio = pca.explained_variance_ratio_
if sum(var_ratio) < min_var_explanation:
raise PcaAccuracyException(
'PCA doesn\'t explain enough of the variance in the data')
return pca_result
def calc_hog(fpaths, save=False):
'''
Compute histogram of gradients (HOG). Saves in batches to prevent memory issues.
Input:
fpaths : files on which HOG will be computed
save : if true, output is saved to disk
'''
hogs = np.empty((len(fpaths), 15876))
for i, fpath in enumerate(fpaths):
img = imread(os.path.join(imgdir, fpath))
if len(img.shape)==3:
img = rgb2gray(img)
# rescale so all feature vectors are the same length
img_resize = resize(img, (128, 128))
img_hog = hog(img_resize)
hogs[i, :] = img_hog
hogs_sc = scale(hogs)
n_components = 15
pca = RandomizedPCA(n_components=n_components)
hogs_decomp = pca.fit_transform(hogs_sc)
df = pd.DataFrame(hogs_decomp, index=[os.path.split(i)[1] for i in fpaths])
df.index.name='fpath'
df.columns = ['feat_hog_%2.2u' % i for i in range(1, n_components+1)]
if save: df.to_csv('hog.csv')
return df
def Q4():
data = datasets.fetch_olivetti_faces(shuffle=True, random_state=0)
X = data.data
y = data.target
image_shape = (64, 64)
n = X.shape[0]
n_components = 10
model = RandomizedPCA(n_components=n_components)
Z = model.fit_transform(X)
Z_c = Z #- Z.mean(axis=1).reshape((n, 1)) !!!! ERROR IN COURSERA
Z_c = Z_c * Z_c
Z_tot = Z_c.sum(axis=1).reshape((n, 1))
Cos = Z_c / Z_tot
i_s = []
for j in range(n_components):
i = np.argmax(Cos[:, j])
i_s.append(i)
image = X[i, :].reshape(image_shape)
#plt.imshow(image)
#plt.show()
utils.PATH.SAVE_RESULT((3, 2), (1, 4), i_s)
return
def scatter(data, labels=None, title=None, name=None):
"""2d PCA scatter plot with optional class info
Return the pca model to be able to introspect the components or transform
new data with the same model.
"""
data = atleast2d_or_csr(data)
if data.shape[1] == 2:
# No need for a PCA:
data_2d = data
else:
pca = RandomizedPCA(n_components=2)
data_2d = pca.fit_transform(data)
for i, c, m in zip(np.unique(labels), cycle(COLORS), cycle(MARKERS)):
plt.scatter(data_2d[labels == i, 0], data_2d[labels == i, 1],
c=c, marker=m, label=i, alpha=0.5)
plt.legend(loc='best')
if title is None:
title = "2D PCA scatter plot"
if name is not None:
title += " for " + name
plt.xlabel('First Principal Component')
plt.ylabel('Second Principal Component')
plt.title(title)
return pca
def main():
protein = sys.argv[1]
X = load_file(protein)
"""
scores = np.loadtxt("../LSDMap/{protein}.scores.txt".format(**locals()))
if scores.shape[0] != RMSD.shape[0]:
scores = scores[-RMSD.shape[0]:]
print("selecting last N")
models = select_N_models(RMSD[1:,1:], scores, 10000)
keep = np.r_[0, models + 1]
n_neigh = np.min(np.sum(RMSD < 6, axis=0)[models + 1])
RMSD = RMSD[keep,:][:,keep]
"""
#models = np.arange(N)
#np.savetxt("output/{protein}/pca/kept.txt".format(**locals()), models)
#np.save("output/{protein}/pca/RMSD.npy".format(**locals()), RMSD[0,:])
pca = RandomizedPCA(n_components=100, copy=False)
proj = pca.fit_transform(X)
acc_var = calcAccumVar(pca.explained_variance_ratio_)
np.savetxt("output/{protein}/pca/acc_var.txt".format(**locals()), acc_var)
np.save("output/%s/pca/proj.npy" % protein, proj)
np.save("output/{protein}/pca/proj2D.npy".format(**locals()), proj[:, :2])
def pca(self, y):
# select a random subset of Y dimensions (possibly gives robustness as well as speed)
rand_dims = np.sort(
np.random.choice(y.shape[1],
np.minimum(self.tree_params['num_dims_for_pca'],
y.shape[1]),
replace=False))
y_dim_subset = y.take(rand_dims, 1)
pca = RandomizedPCA(n_components=1) # compute for all components
# optional: select a subset of exs (not so important if PCA is fast)
if self.tree_params['sub_sample_exs_pca']:
rand_exs = np.sort(
np.random.choice(y.shape[0],
np.minimum(
self.tree_params['num_exs_for_pca'],
y.shape[0]),
replace=False))
pca.fit(y_dim_subset.take(rand_exs, 0))
return pca.transform(y_dim_subset)
else:
# perform PCA
return pca.fit_transform(y_dim_subset)
def dimentionality_reduction(train_x , test_x): print "Dimentionality reduction to 10D on training and test data...." pca = RandomizedPCA(n_components=10) train_x = pca.fit_transform(train_x) test_x = pca.transform(test_x) print "Done." return train_x , test_x
def randomized_pca(train_data_images, train_data_split_images,
test_data_images, IMG_SIZE):
train_data_features = []
test_data_features = []
train_data = []
test_data = []
train_data_split_crossfold = []
for image in train_data_images:
img = img_to_matrix(image, IMG_SIZE)
img = flatten_image(img)
train_data.append(img)
for image in train_data_split_images:
img = img_to_matrix(image, IMG_SIZE)
img = flatten_image(img)
train_data_split_crossfold.append(img)
for image in test_data_images:
img = img_to_matrix(image, IMG_SIZE)
img = flatten_image(img)
test_data.append(img)
pca = RandomizedPCA(50)
return (pca.fit_transform(train_data), pca.transform(test_data))
def dimentionality_reduction(train_x, test_x):
print "Dimentionality reduction to 10D on training and test data...."
pca = RandomizedPCA(n_components=10)
train_x = pca.fit_transform(train_x)
test_x = pca.transform(test_x)
print "Done."
return train_x, test_x
def pca_knn():
Xtrain,ytrain,Xtest,ytest = getSplitData()
Xtrain, Xtest = getScaledData(Xtrain, Xtest)
ntest = Xtest.shape[0]
#Your code here
for n in range(5,8):
pca = RandomizedPCA(n_components=n)
pca_Xtrain = pca.fit_transform(Xtrain, ytrain)
pca_Xtest = pca.fit_transform(Xtest)
neigh = KNeighborsClassifier(n_neighbors=5)
neigh.fit(pca_Xtrain, ytrain)
yPredict = neigh.predict(pca_Xtest)
print "parameter: n_components = ",n
print "parameter: n_neighbors = 5"
print "pca_knn classification accuracy: ", accuracy_score(ytest,yPredict)
def run_pca(self, features):
"""Run a principal component analysis on the training data
"""
pca = RandomizedPCA(n_components=5)
feautres_pca = pca.fit_transform(features)
return feautres_pca
def main():
#get the file path from the command prompt
if len(sys.argv) > 1:
TEST_FILE = sys.argv[1]
else:
print("error: lease specify a file path")
exit()
print("TRAINING STARTED!")
print("pulling images from files...")
#Store image paths and labels
images = []
rawlabels = []
for subdir, dirs, files in os.walk(DATA_DIR):
for file in files:
if (subdir.split('/')[1]) != "test":
rawlabels.append(subdir.split('/')[1])
images.append(os.path.join(subdir, file))
print("converting images to arrays...")
#Create a massive data array
data = []
labels = []
counter = 0
for imagePath in images:
#print imagePath
img = []
try:
img = imgToArray(imagePath)
data.append(img)
labels.append(rawlabels[counter])
except IOError:
pass
counter += 1
data = np.array(data)
print("reducing arrays using randomizedPCA...")
#randomizedPCA on training set
#this reduces the huge amount of data points
pca = RandomizedPCA(n_components=4)
data = pca.fit_transform(data)
#generate a 2D plot that shows the groupings
#generatePlot(data,labels)
print("using K-closest neighbors to classify data...")
#fit the KNeighbors classifier
knn = KNeighborsClassifier()
knn.fit(data, labels)
print("-----------------------------------")
print("TESTING STARTED!")
#test the image
print "The test image, " + TEST_FILE + " is a:"
test = string_to_img(TEST_FILE, pca)
print classify_image(test, knn)
def rca1_decompose(dataset, n):
rca = RandomizedPCA(n_components=n)
reduced_features = rca.fit_transform(dataset.all.features)
training_size = dataset.training_size
training = Data(reduced_features[:training_size, :],
dataset.all.target[:training_size])
testing = Data(reduced_features[training_size:, :],
dataset.all.target[training_size:])
return DataSet(training, testing)
def pca_knn():
Xtrain, ytrain, Xtest, ytest = getSplitData()
Xtrain, Xtest = getScaledData(Xtrain, Xtest)
ntest = Xtest.shape[0]
#Your code here
for n in range(5, 8):
pca = RandomizedPCA(n_components=n)
pca_Xtrain = pca.fit_transform(Xtrain, ytrain)
pca_Xtest = pca.fit_transform(Xtest)
neigh = KNeighborsClassifier(n_neighbors=5)
neigh.fit(pca_Xtrain, ytrain)
yPredict = neigh.predict(pca_Xtest)
print "parameter: n_components = ", n
print "parameter: n_neighbors = 5"
print "pca_knn classification accuracy: ", accuracy_score(
ytest, yPredict)
def fit(self, X, y=None, c=None):
"""Fit the model using X as training data.
Parameters
----------
X : array, shape (n_samples, n_features) or (n_samples, n_samples)
If the metric is 'precomputed' X must be a square distance
matrix. Otherwise it contains a sample per row.
"""
X = check_array(X, accept_sparse=['csr', 'csc', 'coo'], dtype=np.float64)
random_state = check_random_state(self.random_state)
if self.early_exaggeration < 1.0:
raise ValueError("early_exaggeration must be at least 1, but is "
"%f" % self.early_exaggeration)
if self.n_iter < 200:
raise ValueError("n_iter should be at least 200")
if self.metric == "precomputed":
if self.init == 'pca':
raise ValueError("The parameter init=\"pca\" cannot be used "
"with metric=\"precomputed\".")
if X.shape[0] != X.shape[1]:
raise ValueError("X should be a square distance matrix")
distances = X
else:
if self.verbose:
print("[t-SNE] Computing pairwise distances...")
if self.metric == "euclidean":
distances = pairwise_distances(X, metric=self.metric, squared=True)
else:
distances = pairwise_distances(X, metric=self.metric)
# Degrees of freedom of the Student's t-distribution. The suggestion
# alpha = n_components - 1 comes from "Learning a Parametric Embedding
# by Preserving Local Structure" Laurens van der Maaten, 2009.
alpha = max(self.n_components - 1.0, 1)
n_samples = X.shape[0]
self.training_data_ = X
P = _joint_probabilities(distances, self.perplexity, self.verbose)
self.P = deepcopy(P)
if self.init == 'pca':
pca = RandomizedPCA(n_components=self.n_components,
random_state=random_state)
X_embedded = pca.fit_transform(X)
elif self.init == 'random':
X_embedded = None
else:
raise ValueError("Unsupported initialization scheme: %s"
% self.init)
self.embedding_ = self._tsne(P, alpha, n_samples, random_state,
X_embedded=X_embedded, c=c)
def trainset(data, labels):
pca = RandomizedPCA(n_components=10)
std = StandardScaler()
data = np.reshape(data, (data.shape[0], -1))
data = pca.fit_transform(data)
data = std.fit_transform(data)
knn = KNeighborsClassifier()
knn.fit(data, labels)
return pca, std, knn
def visualize():
pca = RandomizedPCA(n_components=2)
X = pca.fit_transform(data)
df = pd.DataFrame({"x": X[:, 0], "y": X[:, 1], "label": labels})
colors = ["red", "yellow"]
for label, color in zip(df['label'].unique(), colors):
mask = df['label'] == label
pl.scatter(df[mask]['x'], df[mask]['y'], c=color, label=label)
pl.legend()
pl.show()
def visualize():
pca = RandomizedPCA(n_components=2)
X = pca.fit_transform(data)
df = pd.DataFrame({"x": X[:, 0], "y": X[:, 1], "label":labels})
colors = ["red", "yellow"]
for label, color in zip(df['label'].unique(), colors):
mask = df['label']==label
pl.scatter(df[mask]['x'], df[mask]['y'], c=color, label=label)
pl.legend()
pl.show()
def HSV_PCA(image_paths, hue_bins = 180, sat_bins = 256, val_bins = 256):
hsv_hists = HSV_hists(image_paths, hue_bins, sat_bins, val_bins)
pca = RandomizedPCA(n_components=3)
hue_pca = pca.fit_transform(np.log(hsv_hists[0]))
sat_pca = pca.fit_transform(np.log(hsv_hists[1]))
val_pca = pca.fit_transform(np.log(hsv_hists[2]))
hsv_df = pd.DataFrame(data = np.hstack((hue_pca, sat_pca, val_pca)))
h_cols = ["HuePC" + str(i) for i in range(1,4)]
s_cols = ["SatPC" + str(i) for i in range(1,4)]
v_cols = ["ValPC" + str(i) for i in range(1,4)]
hsv_df.columns = h_cols + s_cols + v_cols
df_res = pd.concat([pd.DataFrame({'image_paths': image_paths}), hsv_df], axis = 1)
return df_res
def get_pca(data, num_components=2):
"""
Perform a PCA transformation
Parameters
----------
data: Values to transform
num_components: Number of dimension of the data
"""
pca = RandomizedPCA(n_components=num_components, whiten=False)
data = pca.fit_transform(data)
return data, pca.explained_variance_ratio_
def get_input_pca(imgs, labels, pca=None):
I = np.rollaxis(imgs, 2)
I = np.reshape(I, (I.shape[0], -1))
if not pca:
pca = RandomizedPCA(n_components=None, copy=False, iterated_power=3, whiten=False)
I = pca.fit_transform(I)
L = np.ravel(labels)
return I, L, pca
def RPCA(model_data, components=None, transform_data=None):
t0 = time()
rpca = RandomizedPCA(n_components=components)
if transform_data == None:
projection = rpca.fit_transform(model_data)
else:
rpca.fit(model_data)
projection = rpca.transform(transform_data)
print "Randomized PCA Explained Variance: ", rpca.explained_variance_ratio_
print "Randomized PCA Time: %0.3f" % (time() - t0)
return projection
def PlotPCA(self):
pca = RandomizedPCA(n_components=1)
print shape(self.fmri_train)
pca.fit(self.fmri_train)
print shape(pca.components_)
trainingVector = pca.fit_transform(self.fmri_train)
plt.plot(pca.explained_variance_ratio_)
plt.show()
#print pca.get_params()
print shape(trainingVector)
io.mmwrite('fmri_train_240samples_1components.out', trainingVector, field='real', precision=25)
def RPCA(model_data, components = None, transform_data = None):
t0 = time()
rpca = RandomizedPCA(n_components=components)
if transform_data == None:
projection = rpca.fit_transform(model_data)
else:
rpca.fit(model_data)
projection = rpca.transform(transform_data)
print "Randomized PCA Explained Variance: ", rpca.explained_variance_ratio_
print "Randomized PCA Time: %0.3f" % (time() - t0)
return projection
def pca_LG(train, test):
y = []
x_train, y_train, x_test, y_test = split_data(train, test)
pca = RandomizedPCA(n_components=500)
x_train = pca.fit_transform(x_train)
x_test = pca.transform(x_test)
lr = LogisticRegression()
lr.fit(x_train, y_train)
y = lr.predict(x_test)
#print(lr.score(x_train,y_train))
return format_y(y)
def pca_knn(train, test):
y = []
x_train, y_train, x_test, y_test = split_data(train, test)
pca = RandomizedPCA(n_components=2)
x_train = pca.fit_transform(x_train)
x_test = pca.transform(x_test)
knn = KNeighborsClassifier()
knn.fit(x_train, y_train)
y = knn.predict(x_test)
#print(knn.score(x_test,y_test))
return format_y(y)
def test_do_pca(self):
pca_res = do_pca(self.dup_data, 3)
for datum in pca_res.reshape(-1, 1):
self.assertAlmostEqual(datum[0], 0.)
pca_res = do_pca(self.data, 2).reshape(1, -1)[0]
expected_pca = PCA(n_components = 2)
expected_res = expected_pca.fit_transform(self.data).reshape(1, -1)[0]
for expected, actual in zip(expected_res, pca_res):
self.assertAlmostEqual(expected, actual)
def maybeReduceDimensionality(self, img_data):
"""Dimensional reduction of 3D image matrix (numpy array)."""
# Iterating through a ndimensional array produces slices along
# the last axis. This is equivalent to data[i,:,:] in this case
img_data = img_data[::self.n_slices]
if self.reduction is None:
"""No Reduction"""
return img_data
elif self.reduction == "H":
"""Histogram"""
from sklearn import preprocessing
img_data = np.asarray(img_data, dtype=float).flat
min_max_scaler = preprocessing.MinMaxScaler()
scaled_data = min_max_scaler.fit_transform(img_data)
hist = np.histogram(scaled_data,
bins=self.reduction_dict["H"]["value"],
range=None,
normed=False,
weights=None,
density=None)[0]
return hist.reshape(1, hist.shape[0])
elif self.reduction == "P":
"""Slice-wise (randomized) Principal Component Analysis"""
from sklearn.preprocessing import normalize
from sklearn.decomposition import RandomizedPCA
proj_data = []
for img_slice in img_data:
norm_data = normalize(img_slice)
shaped_data = np.reshape(norm_data, norm_data.size)
# shaped_data.shape
rpca = RandomizedPCA(
n_components=self.reduction_dict["P"]["value"],
random_state=0)
proj_slice = rpca.fit_transform(norm_data)
# plt.imshow(proj_data)
# feat_data = rpca.inverse_transform(proj_data)
# plt.imshow(feat_data)
# plt.imshow(norm_data)
proj_data.append(proj_slice)
return proj_data
def pca(data,ncomp=100,whiten=False):
pt4 = time.time()
print 'import and normalization took time {0}'.format(pt4 - pt0)
if whiten == True: #if data needs to be pca whitened, whiten data
pca = RandomizedPCA(n_components=ncomp, whiten=True) #create pca object to pca whiten features
X = pca.fit_transform(data)
else:
X = data #else return data as is
pt5 = time.time()
print 'array cast and pca whitening took time {0}'.format(pt5 - pt2)
print 'total time taken {0}'.format(pt5-pt0)
return X
def plot_for_2d(data , y):
print "Reducing dimension to 2D for visualization...."
pca = RandomizedPCA(n_components=2)
X = pca.fit_transform(data)
df = pd.DataFrame({"x": X[:, 0], "y": X[:, 1], "label":np.where(y==1, "Sphere", "cube")})
colors = ["red", "yellow"]
print "Displaying plot...."
for label, color in zip(df['label'].unique(), colors):
mask = df['label'] == label
pl.scatter(df[mask]['x'], df[mask]['y'], c=color, label=label)
pl.show()
print "Done."
def reduce_dimensions(data, n, random_state=None):
"""
Reduces the input data's dimension to 'n'.
Args:
data: An M x N matrix, where M is the number of samples and N is the number
of features. The dimensions will be reduced from N to n.
n: The new number of dimensions
Returns:
data: An M x n reduced dimension matrix.
"""
pca = RandomizedPCA(n_components=n, random_state=random_state)
return pca.fit_transform(data)
def pcaPic(data, label):
n_components =100
print(data.shape)
print("train pca!!")
pca = RandomizedPCA(n_components=n_components, whiten=True).fit(data)
X_train_pca = pca.fit_transform(data)
y_train = label
print("Fitting the classifier to the training set")
param_grid = {'C': [1e3, 5e3, 1e4, 5e4, 1e5],
'gamma': [0.0001, 0.0005, 0.001, 0.005, 0.01, 0.1], }
clf = GridSearchCV(SVC(kernel='rbf', class_weight='auto'), param_grid)
clf = clf.fit(X_train_pca, y_train)
return pca, clf
def compute_pca(raw_data):
# randomly order the data
# seed(0)
print('shuffling data...')
shuffle(raw_data)
# pull out the features and the labels
print('pulling out data to run PCA...')
data = np.array([cd for (cd, _y, f) in raw_data])
print('finding principal components...')
pca = RandomizedPCA(n_components=N_COMPONENTS, random_state=0)
X = pca.fit_transform(data)
return raw_data, data, pca, X
def preprocess_data():
datasets = sio.loadmat('../multi_data/Hyper_01_Urban.mat')
hypercube = datasets['Hypercube']
datasets = sio.loadmat('../multi_data/Hyper_01_Urban_GroundTruth.mat')
ground_truth = datasets['Ground_Truth']
del datasets
hypercube_1D = np.reshape(hypercube, (-1, hypercube.shape[2]))
rpca = RandomizedPCA(n_components=10, whiten=True)
hypercube_1D_reduced = rpca.fit_transform(hypercube_1D)
hypercube_reduced = np.reshape(
hypercube_1D_reduced, (hypercube.shape[0], hypercube.shape[1], -1))
print rpca.explained_variance_ratio_.sum()
window_sz = 5
window_pad = 2
dataset_matrix_size = ((hypercube_reduced.shape[0] - window_pad) *
(hypercube_reduced.shape[1] - window_pad),
window_sz, window_sz, hypercube_reduced.shape[2])
dataset_matrix = np.zeros(dataset_matrix_size)
label_vector = np.zeros((dataset_matrix.shape[0], ))
data_index = 0
for r in range(hypercube_reduced.shape[0]):
if r < window_pad or r > hypercube_reduced.shape[0] - window_pad - 1:
continue
for c in range(hypercube_reduced.shape[1]):
if c < window_pad or c > hypercube_reduced.shape[
1] - window_pad - 1:
continue
patch = hypercube_reduced[r - window_pad:r + window_pad + 1,
c - window_pad:c + window_pad + 1]
dataset_matrix[data_index, :, :, :] = patch
label_vector[data_index] = ground_truth[r, c]
data_index = data_index + 1
dataset_matrix_r = dataset_matrix[label_vector > 0, :, :, :]
label_vector_r = label_vector[label_vector > 0]
rand_perm = np.random.permutation(label_vector_r.shape[0])
dataset_matrix_r = dataset_matrix_r[rand_perm, :, :, :]
label_vector_r = label_vector_r[rand_perm]
label_vector_r = label_vector_r - 1.0
return dataset_matrix, label_vector, dataset_matrix_r, label_vector_r
def c_random_pca():
pca_2 = RandomizedPCA(n_components=2)
X_pca = pca_2.fit_transform(iris.data)
print(X_pca.shape)
plt.scatter(X_pca[:, 0], X_pca[:, 1], c=iris.target, edgecolors="none")
plt.show()
# Percentage of variance explained by each of the selected components.
# If all components are stored, the sum of explained variances is equal
# to 1.0.
print(pca_2.explained_variance_ratio_.sum())
# Principal axes in feature space, representing the directions of
# maximum variance in the data
print(pca_2.components_)
def pca(all_corr, pc_start, pc_end):
pca_components = pc_end - pc_start
pca = RandomizedPCA(n_components=pca_components, whiten=False)
print 'reducing dimensions to ' + str(pca_components) + ' PCA components'
pc_idx = range(pc_start, pc_end)
pca_xform = pca.fit_transform(all_corr)
all_corr_pca = pca_xform[:, pc_idx] #do not whiten PCA-space data
eig = pca.components_
variances = pca.explained_variance_ratio_
eigenmaps = np.zeros([pca_components, masky * maskx])
eigenmaps[:] = np.nan
eigenmaps[:, pushmask] = eig
eigenmaps_img = eigenmaps.reshape(pca_components, masky, maskx)
return eigenmaps_img, all_corr_pca, variances
def test_non_square_infomax():
""" Test non-square infomax
"""
from sklearn.decomposition import RandomizedPCA
rng = np.random.RandomState(0)
n_samples = 200
# Generate two sources:
t = np.linspace(0, 100, n_samples)
s1 = np.sin(t)
s2 = np.ceil(np.sin(np.pi * t))
s = np.c_[s1, s2].T
center_and_norm(s)
s1, s2 = s
# Mixing matrix
n_observed = 6
mixing = rng.randn(n_observed, 2)
for add_noise in (False, True):
m = np.dot(mixing, s)
if add_noise:
m += 0.1 * rng.randn(n_observed, n_samples)
center_and_norm(m)
pca = RandomizedPCA(n_components=2, whiten=True, random_state=rng)
m = m.T
m = pca.fit_transform(m)
# we need extended since input signals are sub-gaussian
unmixing_ = infomax(m, random_state=rng, extended=True)
s_ = np.dot(unmixing_, m.T)
# Check that the mixing model described in the docstring holds:
mixing_ = linalg.pinv(unmixing_.T)
assert_almost_equal(m, s_.T.dot(mixing_))
center_and_norm(s_)
s1_, s2_ = s_
# Check to see if the sources have been estimated
# in the wrong order
if abs(np.dot(s1_, s2)) > abs(np.dot(s1_, s1)):
s2_, s1_ = s_
s1_ *= np.sign(np.dot(s1_, s1))
s2_ *= np.sign(np.dot(s2_, s2))
# Check that we have estimated the original sources
if not add_noise:
assert_almost_equal(np.dot(s1_, s1) / n_samples, 1, decimal=2)
assert_almost_equal(np.dot(s2_, s2) / n_samples, 1, decimal=2)
def get_pca_data_batch(imgs, hight=resize_hight, width=resize_width):
"""
"""
newsize = (hight, width)
rImgs = [lib_cv2.resize(e, newsize) for e in imgs]
rImgs = [lib_cv2.cvtColor(e, lib_cv2.COLOR_BGR2GRAY) for e in rImgs]
rImgs = [e.ravel() for e in rImgs]
pca = RandomizedPCA(n_components=200, whiten=True)
pImgs = pca.fit_transform(rImgs)
return pImgs