def test_init_with_correct_file_input(self):
"""
Ensure a valid dict is created from a correct json during init
"""
settings = utils.Settings(self.check_settings_file)
self.assertIs(settings.user_input.__class__, dict)
self.assertTrue(len(settings.user_input) > 0)
def test_resolves_to_correct_dir(self):
"""
Make sure settings parser resolves to dir containing test and train dirs
"""
settings_string_with_2_dirs = io.StringIO(
u'{"data_dir": ["fake", "TestSettingsParserDir"]}')
settings = utils.Settings(settings_string_with_2_dirs)
self.assertEqual(settings.data_dir, os.path.abspath(self.data_dir))
def test_error_if_required_missing(self):
"""
Ensure error is thrown if a required setting is omitted
"""
setting_string_without_required = io.StringIO(
u'{"foo": 5, "bar": "duck"}')
with self.assertRaises(ValueError):
utils.Settings(setting_string_without_required)
def check_default_values_during_init(self):
"""
Make sure default values are set for r_seed
"""
settings = utils.Settings(self.check_settings_file)
classes = constants.classes
self.assertIs(settings.random_seed, 42)
self.assertIs(settings.classes, classes)
def test_init_with_correct_stringIO(self):
"""
Ensure a valid dict is created from a correct json io.String during init
"""
string_settings = io.StringIO(
u'{"data_dir": ["TestSettingsParserDir"]}')
settings = utils.Settings(string_settings)
self.assertIs(settings.user_input.__class__, dict)
self.assertTrue(len(settings.user_input) > 0)
def main():
# this should be parsed from json, but hardcoded for now
#attributes_settings = ['width','height']
#pkl_file = 'imsizeLR.pkl'
#attributes_settings = ['numpixels','aspectratio']
#pkl_file = 'imsizeLR_alt.pkl'
attributes_settings = ['width','height','mean','stderr','propwhite','propbool','propblack']
pkl_file = 'imattr1.pkl'
# Load the settings, providing
settings = utils.Settings('settings.json')
# Make the wrapper function
processing = highlevelfeatures.BasicAttributes(attributes_settings)
# Load the training data, with the processing applied
X, y = utils.load_data(settings.image_fnames, classes=settings.classes,
processing=processing)
# Encode the labels
label_encoder = sklearn.preprocessing.LabelEncoder()
y = label_encoder.fit_transform(y)
# just a dummy uniform probability classifier for working purposes
#clf = sklearn.dummy.DummyClassifier(strategy='uniform')
#clf = sklearn.linear_model.SGDClassifier(n_jobs=-1,
# loss='log')
#clf = sklearn.ensemble.RandomForestClassifier(n_jobs=-1,
# n_estimators=100,
# verbose=1)
# clf = sklearn.svm.SVC(probability=True)
clf = sklearn.linear_model.LogisticRegression()
cv = sklearn.cross_validation.StratifiedShuffleSplit(y)
# Try cross-validating
results = []
for train, test in cv:
clf.fit(X[train], y[train])
p = clf.predict_proba(X[test])
results.append(sklearn.metrics.log_loss(y[test], p))
print(results)
print('CV average = {}'.format(np.mean(results)))
# Train on the whole thing and save model for later
clf.fit(X,y)
joblib.dump(clf, pkl_file, compress=3)
def main(run_settings_path, verbose=False, force=False):
# load the non-run-specific settings
settings = utils.Settings('settings.json')
# load the run-specific settings
run_settings = utils.load_run_settings(run_settings_path,
settings,
settings_path='settings.json',
force=force)
if run_settings['model type'] == 'sklearn':
train_sklearn(run_settings, verbose=verbose, force=force)
elif run_settings['model type'] == 'pylearn2':
train_pylearn2(run_settings, verbose=verbose, force=force)
else:
raise NotImplementedError("Unsupported model type.")
def main(run_settings_path, verbose=False, altdata=None, augment=1, split=1):
# this should just run either function depending on the run settings
settings = utils.Settings('settings.json')
# test script won't overwrite the pickle, so always force load
run_settings = utils.load_run_settings(run_settings_path,
settings,
settings_path='settings.json',
force=True)
# HELLO BOILERPLATE
if run_settings['model type'] == 'sklearn':
test_sklearn(run_settings, verbose=verbose)
elif run_settings['model type'] == 'pylearn2':
#train_pylearn2(run_settings)
test_pylearn2(run_settings, verbose=verbose,altdata=altdata,
augment=augment, split=split)
else:
raise NotImplementedError("Unsupported model type.")
def main():
# yeah, that ought to parse it
settings = utils.Settings('settings.json')
# loading in mnist
train_path = os.path.join(settings.data_dir, "mnist_train.npz")
test_path = os.path.join(settings.data_dir, "mnist_test.npz")
train_npz = np.load(train_path)
test_npz = np.load(test_path)
# sticking it all together
X = np.vstack([train_npz['arr_0'], test_npz['arr_0']])
y = np.hstack([train_npz['arr_1'], test_npz['arr_1']])
# Testing out the mlp function
mlp = neukrill_net.nk_mlp.MLP_sk_interface(verbose=True)
mlp.fit(X, y)
def main():
# this should be parsed from json, but hardcoded for now
#attributes_settings = ['width','height']
#pkl_file = 'imsizeLR.pkl'
#out_fname = 'submission_imsizeLR.csv'
#attributes_settings = ['width','height']
#pkl_file = 'imsizeSVM.pkl'
#out_fname = 'submission_imsizeSVM.csv'
#attributes_settings = ['numpixels','aspectratio']
#pkl_file = 'imsizeLR_alt.pkl'
#out_fname = 'submission_imsizeLR_alt.csv'
attributes_settings = [
'width', 'height', 'mean', 'stderr', 'propwhite', 'propbool',
'propblack'
]
pkl_file = 'imattr1.pkl'
out_fname = 'submission_imattr1.csv'
# Get global settings, providing file names of test data
settings = utils.Settings('settings.json')
# Make the wrapper function
processing = highlevelfeatures.attributes_wrapper(attributes_settings)
# Load the test data, with the processing applied
X, names = utils.load_data(settings.image_fnames,
processing=processing,
verbose=False)
clf = joblib.load(pkl_file)
p = clf.predict_proba(X)
utils.write_predictions(out_fname, p, names, settings.classes)
def main():
out_fname = 'submission_priorprobs.csv'
settings = utils.Settings('settings.json')
# Get names of test data files
names = [
os.path.basename(fpath) for fpath in settings.image_fnames['test']
]
# Score expected from training data (not a CV score because no folds)
labels = []
for class_index, class_name in enumerate(settings.classes):
num_images = len(settings.image_fnames['train'][class_name])
# generate the class labels and add them to the list
labels += num_images * [class_name]
p = settings.class_priors[np.newaxis, :]
p = np.tile(p, (len(labels), 1))
label_encoder = sklearn.preprocessing.LabelEncoder()
y = label_encoder.fit_transform(labels)
cv = sklearn.metrics.log_loss(y, p)
print('CV = {}'.format(cv))
# Write output
with open(out_fname, 'w') as csv_out:
out_writer = csv.writer(csv_out, delimiter=',')
out_writer.writerow(['image'] + list(settings.classes))
for index in range(len(names)):
out_writer.writerow([names[index]] + list(settings.class_priors))
with open(out_fname, 'rb') as f_in:
f_out = gzip.open(out_fname + '.gz', 'wb')
f_out.writelines(f_in)
f_out.close()
def main():
# this should be parsed from json, but hardcoded for now
bow_options = {
'verbose': True,
'normalise_hist': False,
'n_features_max': 100,
'patch_size': 15,
'clusteralgo': 'kmeans',
'n_clusters': 20,
'random_seed': 42
}
# Load the settings, providing
settings = utils.Settings('settings.json')
# Load the raw data
print('Loading the raw training data')
rawdata, labels = utils.load_rawdata(settings.image_fnames,
classes=settings.classes)
# Encode the labels
label_encoder = sklearn.preprocessing.LabelEncoder()
y = label_encoder.fit_transform(labels)
# Probably not the best classifier
clf = sklearn.linear_model.LogisticRegression()
cv = sklearn.cross_validation.StratifiedShuffleSplit(y)
bow = highlevelfeatures.BagOfWords(**bow_options)
sample = np.random.random_integers(
0, len(rawdata) - 1,
size=(1000)) # Subsample so we can do this in sensible time
bow.fit([rawdata[i] for i in sample])
#bow.fit(rawdata)
print('Bagging words for raw training data')
X = bow.extractfeatures(rawdata)
X = np.squeeze(X)
# Try cross-validating
print('Cross-validating')
results = []
for train, test in cv:
# Make a new BOW encoding
#bow = highlevelfeatures.BagOfWords(**bow_options)
#bow.fit([rawdata[i] for i in train])
#X = bow.extractfeatures(rawdata)
clf.fit(X[train, :], y[train])
p = clf.predict_proba(X[test])
res = sklearn.metrics.log_loss(y[test], p)
print(res)
results.append(res)
print(results)
print('CV average = {}'.format(np.mean(results)))
# Train on the whole thing and save model for later
#bow = highlevelfeatures.BagOfWords(**bow_options)
#bow.fit(rawdata)
#X = bow.extractfeatures(rawdata)
clf.fit(X, y)
print('Loading the raw test data')
rawtest, names = utils.load_rawdata(settings.image_fnames)
print('Bagging words for raw test data')
X2 = X = bow.extractfeatures(rawdata)
X2 = np.squeeze(X2)
p = clf.predict_proba(X2)
utils.write_predictions('submission_bow_initial.csv', p, names,
settings.classes)
def test_error_if_file_does_not_exist(self):
"""
Ensure an IOError is thrown if the file doesn't exist
"""
with self.assertRaises(ValueError):
utils.Settings('fake_file')