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authorVasil Zlatanov <vz215@eews506a-024.ee.ic.ac.uk>2018-11-04 17:32:19 +0000
committerVasil Zlatanov <v@skozl.com>2018-11-05 15:53:47 +0000
commit09630bb27dec915fbe59385755d62809bcfd689e (patch)
treebcabd6e9d8dbc521fb815722a87052025315bf77
parent93f09de3f1ba422758ce679ce99ad0ac17d8d4a5 (diff)
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Refactor code and use timing
-rwxr-xr-xtrain.py278
1 files changed, 150 insertions, 128 deletions
diff --git a/train.py b/train.py
index 5530664..064d92e 100755
--- a/train.py
+++ b/train.py
@@ -2,6 +2,8 @@
# Train a model from sample data
# Author: Vasil Zlatanov, Nunzio Pucci
# EE4 Pattern Recognition coursework
+#
+# usage: train.py [-h] -i DATA -o MODEL [-m M]
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
@@ -14,7 +16,7 @@ from sklearn.decomposition import PCA
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import StandardScaler
-from sklearn.metrics import confusion_matrix
+from sklearn.metrics import confusion_matrix
from sklearn.metrics import accuracy_score
import argparse
@@ -23,16 +25,21 @@ import numpy as np
from numpy import genfromtxt
from numpy import linalg as LA
+from timeit import default_timer as timer
+
+n_faces = 52
+n_cases = 10
+n_pixels = 2576
+
# subtract the normal face from each row of the face matrix
def normalise_faces(average_face, faces):
faces = np.subtract(faces, np.tile(average_face, (faces.shape[0],1)))
return np.divide(faces.T, np.std(faces.T, axis=0)).T
+
# Split data into training and testing sets
def test_split(n_faces, raw_faces, split, seed):
random.seed(seed)
- n_cases = 10
- n_pixels = 2576
-
+
raw_faces_split = np.split(raw_faces,n_cases)
n_training_faces = int(round(n_cases*(1 - split)))
n_test_faces = n_cases - n_training_faces
@@ -40,139 +47,154 @@ def test_split(n_faces, raw_faces, split, seed):
faces_test = np.zeros((n_faces, n_test_faces, n_pixels))
target_train = np.repeat(np.arange(n_faces), n_training_faces)
target_test = np.repeat(np.arange(n_faces), n_test_faces)
-
- for x in range (n_faces):
+
+ for x in range(n_faces):
samples = random.sample(range(n_cases), n_training_faces)
faces_train[x] = [raw_faces[i+n_cases*x] for i in samples]
- faces_test[x] = [raw_faces[i+n_cases*x] for i in range (n_cases) if i not in samples]
+ faces_test[x] = [raw_faces[i+n_cases*x] for i in range(n_cases) if i not in samples]
faces_train = faces_train.reshape(n_faces*n_training_faces, n_pixels)
faces_test = faces_test.reshape(n_faces*n_test_faces, n_pixels)
return faces_train, faces_test, target_train, target_test
-# usage: train.py [-h] -i DATA -o MODEL [-m M]
-parser = argparse.ArgumentParser()
-parser.add_argument("-i", "--data", help="Input CSV file", required=True)
-parser.add_argument("-m", "--eigen", help="Number of eigenvalues in model", type=int, default = 10 )
-parser.add_argument("-n", "--neighbors", help="How many neighbors to use", type=int, default = 3)
-parser.add_argument("-f", "--faces", help="Show faces", type=int, default = 0)
-parser.add_argument("-c", "--principal", help="Show principal components", action='store_true')
-parser.add_argument("-s", "--seed", help="Seed to use", type=int, default=0)
-parser.add_argument("-t", "--split", help="Fractoin of data to use for testing", type=float, default=0.22)
-### best split for lda = 22
-### best plit for pca = 20
-parser.add_argument("-2", "--grapheigen", help="Swow 2D graph of targets versus principal components", action='store_true')
-parser.add_argument("-p", "--pca", help="Use PCA", action='store_true')
-parser.add_argument("-l", "--lda", help="Use LDA", action='store_true')
-parser.add_argument("-r", "--reconstruct", help="Use PCA reconstruction, specify face NR", type=int, default=0)
-parser.add_argument("-cm", "--conf_mat", help="Show visual confusion matrix", action='store_true')
-
-parser.add_argument("-q", "--pca_r", help="Use Reduced PCA", action='store_true')
-
-args = parser.parse_args()
-
-M = args.eigen
-
-raw_faces = genfromtxt(args.data, delimiter=',')
-targets = np.repeat(np.arange(52),10)
-
-n_faces = 52
-
-faces_train, faces_test, target_train, target_test = test_split(n_faces, raw_faces, args.split, args.seed)
-
-# This remove the mean and scales to unit variance
-sc = StandardScaler()
-#faces_train = sc.fit_transform(faces_train)
-#faces_test = sc.transform(faces_test)
-raw_faces_train = faces_train
-
-explained_variances = ()
-
-if args.pca or args.pca_r:
- # faces_pca containcts the principial components or the M most variant eigenvectors
- average_face = np.mean(faces_train, axis=0)
- deviations_tr = np.std(faces_train, axis=0)
- deviations_tst = np.std(faces_train, axis=0)
- faces_train = normalise_faces(average_face, faces_train)
- faces_test = normalise_faces(average_face, faces_test)
- if (args.pca_r):
- print('Reduced PCA')
- e_vals, e_vecs = LA.eigh(np.dot(faces_train, faces_train.T))
- e_vecs = np.dot(faces_train.T, e_vecs)
- e_vecs = e_vecs/LA.norm(e_vecs, axis = 0)
- else:
- print('Standard PCA')
- e_vals, e_vecs = LA.eigh(np.cov(faces_train.T))
- # e_vecs = normalise_faces(np.mean(e_vecs,axis=0), e_vecs)
- # e_vecs = sc.fit_transform(e_vecs)
-
- e_vals = np.flip(e_vals)[:M]
- e_vecs = np.fliplr(e_vecs).T[:M]
- deviations_tr = np.flip(deviations_tr)
- deviations_tst = np.flip(deviations_tst)
+def draw_conf_mat(target_test, target_pred):
+ cm = confusion_matrix(target_test, target_pred)
+ print(cm)
+ if (args.conf_mat):
+ plt.matshow(cm, cmap='Blues')
+ plt.colorbar()
+ plt.ylabel('Actual')
+ plt.xlabel('Predicted')
+ plt.show()
+ print('Accuracy %fl' % accuracy_score(target_test, target_pred))
+
+def test_model(M, faces_train, faces_test, target_train, target_test, args):
+ raw_faces_train = faces_train
+
+ explained_variances = ()
+
+ if args.pca or args.pca_r:
+ # faces_pca containcts the principial components or the M most variant eigenvectors
+ average_face = np.mean(faces_train, axis=0)
+ deviations_tr = np.std(faces_train, axis=0)
+ deviations_tst = np.std(faces_train, axis=0)
+ faces_train = normalise_faces(average_face, faces_train)
+ faces_test = normalise_faces(average_face, faces_test)
+ if (args.pca_r):
+ print('Reduced PCA')
+ e_vals, e_vecs = LA.eigh(np.dot(faces_train, faces_train.T))
+ e_vecs = np.dot(faces_train.T, e_vecs)
+ e_vecs = e_vecs/LA.norm(e_vecs, axis = 0)
+ else:
+ print('Standard PCA')
+ e_vals, e_vecs = LA.eigh(np.cov(faces_train.T))
+ # e_vecs = normalise_faces(np.mean(e_vecs,axis=0), e_vecs)
+
+ e_vals = np.flip(e_vals)[:M]
+ e_vecs = np.fliplr(e_vecs).T[:M]
+ deviations_tr = np.flip(deviations_tr)
+ deviations_tst = np.flip(deviations_tst)
+
+ faces_train = np.dot(faces_train, e_vecs.T)
+ faces_test = np.dot(faces_test, e_vecs.T)
+
+ if (args.reconstruct):
+ rec_vec = np.add(average_face, np.dot(faces_train[args.reconstruct], e_vecs) * deviations_tr)
+ rec_faces_test = np.add(average_face, np.dot(faces_test, e_vecs) * deviations_tst)
+ rec_error = LA.norm(np.subtract(raw_faces_train[args.reconstruct], rec_vec))
+ ar = plt.subplot(2, 1, 1)
+ ar.imshow(rec_vec.reshape([46,56]).T, cmap = 'gist_gray')
+ ar = plt.subplot(2, 1, 2)
+ ar.imshow(raw_faces_train[args.reconstruct].reshape([46,56]).T, cmap = 'gist_gray')
+ plt.show()
+
+ if args.lda or (args.pca and args.lda):
+ lda = LinearDiscriminantAnalysis(n_components=M, solver='eigen')
+ faces_train = lda.fit_transform(faces_train, target_train)
+ faces_test = lda.transform(faces_test)
+ class_means = lda.means_
+ e_vals = lda.explained_variance_ratio_
+
+ if args.faces:
+ if args.lda:
+ for i in range(10):
+ ax = plt.subplot(2, 5, i + 1)
+ ax.imshow(class_means[i].reshape([46,56]).T)
+ else:
+ for i in range(args.faces):
+ ax = plt.subplot(2, args.faces/2, i + 1)
+ ax.imshow(e_vecs[i].reshape([46, 56]).T, cmap = 'gist_gray')
+ plt.show()
- faces_train = np.dot(faces_train, e_vecs.T)
- faces_test = np.dot(faces_test, e_vecs.T)
+ if args.principal:
+ e_vals = np.multiply(np.divide(e_vals, np.sum(e_vals)), 100)
+ plt.bar(np.arange(M), e_vals[:M])
+ plt.ylabel('Varaiance ratio (%)');plt.xlabel('Number')
+ plt.show()
- if (args.reconstruct):
- rec_vec = np.add(average_face, np.dot(faces_train[args.reconstruct], e_vecs) * deviations_tr)
- rec_faces_test = np.add(average_face, np.dot(faces_test, e_vecs) * deviations_tst)
- rec_error = LA.norm(np.subtract(raw_faces_train[args.reconstruct], rec_vec))
- ar = plt.subplot(2, 1, 1)
- ar.imshow(rec_vec.reshape([46,56]).T, cmap = 'gist_gray')
- ar = plt.subplot(2, 1, 2)
- ar.imshow(raw_faces_train[args.reconstruct].reshape([46,56]).T, cmap = 'gist_gray')
+ if args.grapheigen:
+ graph_eigen()
+ # Colors for distinct individuals
+ cols = ['#{:06x}'.format(randint(0, 0xffffff)) for i in range(n_faces)]
+ pltCol = [cols[int(k)] for k in target_train]
+ fig = plt.figure()
+ ax = fig.add_subplot(111, projection='3d')
+ ax.scatter(faces_train[:, 0], faces_train[:, 1], faces_train[:, 2], marker='o', color=pltCol)
plt.show()
-if args.lda or (args.pca and args.lda):
- lda = LinearDiscriminantAnalysis(n_components=M, solver='eigen')
- faces_train = lda.fit_transform(faces_train, target_train)
- faces_test = lda.transform(faces_test)
- class_means = lda.means_
- e_vals = lda.explained_variance_ratio_
-
-if args.faces:
- if args.lda:
- for i in range (10):
- ax = plt.subplot(2, 5, i + 1)
- ax.imshow(class_means[i].reshape([46,56]).T)
+ classifier = KNeighborsClassifier(n_neighbors=args.neighbors)
+ if (args.reconstruct):
+ classifier.fit(raw_faces_train, target_train)
+ target_pred = classifier.predict(rec_faces_test)
+ #Better Passing n_neighbors = 1
+ else:
+ classifier.fit(faces_train, target_train)
+ target_pred = classifier.predict(faces_test)
+ #Better n_neighbors = 2
+ draw_conf_mat(target_test, target_pred)
+
+def main():
+ parser = argparse.ArgumentParser()
+ parser.add_argument("-i", "--data", help="Input CSV file", required=True)
+ parser.add_argument("-m", "--eigen", help="Number of eigenvalues in model", type=int, default = 10 )
+ parser.add_argument("-M", "--reigen", help="Number of eigenvalues in model", type=int)
+ parser.add_argument("-n", "--neighbors", help="How many neighbors to use", type=int, default = 3)
+ parser.add_argument("-f", "--faces", help="Show faces", type=int, default = 0)
+ parser.add_argument("-c", "--principal", help="Show principal components", action='store_true')
+ parser.add_argument("-s", "--seed", help="Seed to use", type=int, default=0)
+ parser.add_argument("-t", "--split", help="Fractoin of data to use for testing", type=float, default=0.22)
+ ### best split for lda = 22
+ ### best plit for pca = 20
+ parser.add_argument("-2", "--grapheigen", help="Swow 2D graph of targets versus principal components", action='store_true')
+ parser.add_argument("-p", "--pca", help="Use PCA", action='store_true')
+ parser.add_argument("-l", "--lda", help="Use LDA", action='store_true')
+ parser.add_argument("-r", "--reconstruct", help="Use PCA reconstruction, specify face NR", type=int, default=0)
+ parser.add_argument("-cm", "--conf_mat", help="Show visual confusion matrix", action='store_true')
+
+ parser.add_argument("-q", "--pca_r", help="Use Reduced PCA", action='store_true')
+
+ args = parser.parse_args()
+
+ raw_faces = genfromtxt(args.data, delimiter=',')
+ targets = np.repeat(np.arange(n_faces),n_cases)
+
+
+ faces_train, faces_test, target_train, target_test = test_split(n_faces, raw_faces, args.split, args.seed)
+
+
+ if args.reigen:
+ for M in range(args.eigen, args,reigen):
+ start = time()
+ test_model(M, faces_train, faces_test, target_train, target_test, args)
+ end = time()
+ print("Run with", M, "eigenvalues completed in %.2f" % end-start, "seconds")
else:
- for i in range(args.faces):
- ax = plt.subplot(2, args.faces/2, i + 1)
- ax.imshow(e_vecs[i].reshape([46, 56]).T, cmap = 'gist_gray')
- plt.show()
-
-if args.principal:
- e_vals = np.multiply(np.divide(e_vals, np.sum(e_vals)), 100)
- plt.bar(np.arange(M), e_vals[:M])
- plt.ylabel('Varaiance ratio (%)');plt.xlabel('Eigenface Number')
- plt.show()
-
-if args.grapheigen:
- # Colors for distinct individuals
- cols = ['#{:06x}'.format(randint(0, 0xffffff)) for i in range(52)]
- pltCol = [cols[int(k)] for k in target_train]
- fig = plt.figure()
- ax = fig.add_subplot(111, projection='3d')
- ax.scatter(faces_train[:, 0], faces_train[:, 1], faces_train[:, 2], marker='o', color=pltCol)
- plt.show()
-
-classifier = KNeighborsClassifier(n_neighbors=args.neighbors)
-if (args.reconstruct):
- classifier.fit(raw_faces_train, target_train)
- target_pred = classifier.predict(rec_faces_test)
- #Better Passing n_neighbors = 1
-else:
- classifier.fit(faces_train, target_train)
- target_pred = classifier.predict(faces_test)
- #Better n_neighbors = 2
-
-cm = confusion_matrix(target_test, target_pred)
-print(cm)
-if (args.conf_mat):
- plt.matshow(cm, cmap='Blues')
- plt.colorbar()
- plt.ylabel('Actual')
- plt.xlabel('Predicted')
- plt.show()
-print('Accuracy %fl' % accuracy_score(target_test, target_pred))
+ M = args.eigen
+ start = time()
+ test_model(M, faces_train, faces_test, target_train, target_test, args):
+ end = time()
+ print("Run with", M, "eigenvalues completed in %.2f" % end-start, "seconds")
+
+
+if __name__ == "__main__":
+ main()