def sample_bottom_up(infile='presents_revorder.csv', outfile='sub_bottomup_1.csv', write=True, check=True):
"""
Replicate the sample bottom-up approach
"""
sleigh = classes.LayerSleigh()
layer = classes.Layer()
presents_file = os.path.join('data', infile)
outfile = os.path.join('data', outfile)
logger.info("Reading and placing presents")
with open(presents_file, 'rb') as presents:
presents.readline() # skip header
read = csv.reader(presents)
for row in read:
present = classes.Present(*row)
if not layer.place_present(present):
# Can't place the present on the layer, so close the layer and start a new one
sleigh.add_layer(layer)
layer = classes.Layer(z=sleigh.max_z + 1)
res = layer.place_present(present)
# Add the final layer
sleigh.add_layer(layer)
if check and not sleigh.check_all():
logger.error('There is an error in the Sleigh')
return sleigh
if write:
sleigh.write_to_file(outfile)
return sleigh
def sendEmails(self, receiverEmails: List[str], msg: str, subject: str) -> None:
try:
smtpServer = "smtp.gmail.com"
senderEmail = environ.get('SENDEREMAIL')
password = environ.get('EMAILPWD')
if senderEmail and password:
with smtplib.SMTP_SSL(smtpServer, 465) as server:
server.login(senderEmail, password)
for email in receiverEmails:
try:
emailMsg = EmailMessage()
emailMsg.set_content(msg)
emailMsg['Subject'] = subject
emailMsg['From'] = senderEmail
emailMsg['To'] = email
server.send_message(emailMsg)
info("{} Email sent to {}".format(subject, email))
except Exception as e:
# log error
error(str(e))
else:
raise Exception("Missing sender email and/or password")
except Exception as e:
error(str(e))
def delete_db(): #wipe db
try:
tableNameList = [
"User", "Playlists", "Tracks", "Albums", "Artists", "TrackAlbum",
"TrackArtists", "TrackPlaylists", "AlbumArtists"
] #list of tables names
logger.info("DROPPING DATABASE; User Call")
try:
for i in tableNameList:
get_db().execute(f"DROP TABLE {i}") #drop tables
logger.debug(
f"DROPPING {i}; REASON: User Call [Delete Database]")
except sqlite3.OperationalError as e:
logger.warning("RuntimeError; " + e.__str__() +
"; User calling DeleteDB whilst no tables; Ignore")
except RuntimeError as e: #except error if its out of request context
logger.warning("RuntimeError; " + e.__str__() +
"; POSSIBLE REASON: FIRST TIME STARTUP")
logger.warning("Re calling delete_db out of application context")
db = sqlite3.connect(DATABASE) # connect to db out of reqauest context
try:
for i in tableNameList:
db.execute(f"DROP TABLE {i}")
logger.debug(
f"DROPPING {i}; REASON: User Call [Delete Database]")
db.commit()
except sqlite3.OperationalError as e:
logger.debug(e.__str__())
def kmeans_006_colwise_rmse():
crop = 150
s = 15
n_centroids = 3000
images = get_images(crop=crop, s=s)
kmeans_generator = train_kmeans_generator(images, n_centroids=n_centroids)
train_x = kmeans_generator.transform(images, save_to_file='data/data_kmeans_features_006_centroids_{}.npy'.format(n_centroids), memmap=True)
train_y = classes.train_solutions.data
train_x, test_x, train_y, test_y = train_test_split(train_x, train_y, train_size=0.2, test_size=0.2)
# Unload some objects
del images
gc.collect()
wrapper = ModelWrapper(models.Ridge.RidgeRFEstimator, {'alpha': 500, 'n_estimators': 500, 'verbose': 1}, n_jobs=-1)
wrapper.fit(train_x, train_y)
# About 11 minutes to train the ridge regression on an m2.4 xlarge with 50% of the train set
# Took about a minute to train ridge on 0.1 of the train set, but the overall rmse was .114 compared to .106 on 50%, and .104 actual
# 5 minutes to train ridge on 0.2 of the train set, with rmse of .111
kmeans_preds = wrapper.predict(test_x)
logger.info('Kmeans')
colwise = classes.colwise_rmse(kmeans_preds, test_y)
overall = classes.rmse(kmeans_preds, test_y)
"""
def fit(self, X, y):
self.ridge_estimator_ = self._get_ridge_model()
self.rf_estimator_ = self._get_rf_model()
logger.info("Fitting Ridge model")
self.ridge_estimator_.fit(X, y)
ridge_y = self.ridge_estimator_.predict(X)
logger.info("Fitting RF model")
self.rf_estimator_.fit(ridge_y, y)
def predict_test(self, average_responses):
logger.info("Calculating predictions for test set")
# Now calculate the test set responses
test_predictors = self.build_test_predictors()
test_clusters = self.estimator.predict(test_predictors)
test_averages = average_responses[test_clusters]
return test_averages
def build_features(self, files, training=True):
"""
Utility method that loops over every image and applies self.process_image
Returns a numpy array of dimensions (n_observations, n_features)
"""
logger.info("Building predictors")
predictors = self.do_for_each_image(files, self.process_image, self.n_features, training)
return predictors
def fit(self, X, y):
self.ridge_estimator_ = self._get_ridge_model()
self.rf_estimator_ = self._get_rf_model()
logger.info("Fitting Ridge model")
self.ridge_estimator_.fit(X, y)
ridge_y = self.ridge_estimator_.predict(X)
logger.info("Fitting RF model")
self.rf_estimator_.fit(ridge_y, y)
def fit_estimator(self):
# Fit a k-means clustering estimator
# We use 37 centers initially because there are 37 classes
# Seems like the sample submission used 6 clusters
start_time = time.time()
logger.info("Fitting kmeans estimator")
self.estimator = KMeans(init='k-means++', n_clusters=37)
self.estimator.fit(self.predictors)
logger.info("Finished fitting model in {}".format(time.time() - start_time))
def _transform(training, features, file_list):
filepath = TRAIN_IMAGE_PATH if training else TEST_IMAGE_PATH
res = []
for i, f in enumerate(file_list):
if i % 5000 == 0:
logger.info("Processing image {} of {}".format(i, len(file_list)))
img = RawImage(os.path.join(filepath, f))
features = [func(img) for func in features]
res.append(np.hstack(features))
return res
def get_cluster_averages(self):
# Get the average response for each cluster in the training set
# This is a 37 x 37 array, one row for each cluster, and one column for each class
logger.info("Calculating cluster averages")
average_responses = np.zeros((37, 37))
for cluster in range(37):
idx = self.estimator.labels_ == cluster
responses = self.train_y[idx, :]
average_responses[cluster] = responses.mean(axis=0)
logger.info("Finished calculating cluster averages")
return average_responses
def _parallel_sampler(file_list, steps, step_size, training):
filepath = TRAIN_IMAGE_PATH if training else TEST_IMAGE_PATH
rows = []
counter = 0
for i, f in enumerate(file_list):
counter += 1
if counter % 5000 == 0:
logger.info("Processed {} images".format(counter))
image = RawImage(os.path.join(filepath, f))
rows.append(image.grid_sample(step_size, steps).flatten().astype('float64') / 255)
return np.vstack(rows)
def _transform(self, file_list):
filepath = TRAIN_IMAGE_PATH if self.training else TEST_IMAGE_PATH
out = np.zeros((len(file_list), self.scaled_size, self.scaled_size, 3))
factor = self.scaled_size / self.crop_size
for i, f in enumerate(file_list):
if i % 5000 == 0:
logger.info("Processing image {} of {}".format(i, len(file_list)))
img = RawImage(os.path.join(filepath, f))
img.crop(self.crop_size).rescale(factor)
out[i] = img.data * 255
return out
def _transform(training, features, file_list):
filepath = TRAIN_IMAGE_PATH if training else TEST_IMAGE_PATH
res = []
for i, f in enumerate(file_list):
if i % 5000 == 0:
logger.info("Processing image {} of {}".format(
i, len(file_list)))
img = RawImage(os.path.join(filepath, f))
features = [func(img) for func in features]
res.append(np.hstack(features))
return res
def run(self, check=True, write=True):
presents_file = os.path.join('data', self.infile)
outfile = os.path.join('data', self.outfile)
logger.info("Reading and placing presents")
counter = 0
with open(presents_file, 'rb') as presents:
presents.readline() # skip header
read = csv.reader(presents)
for row in read:
present = classes.Present(*row)
position = self.sleigh.place_present(present)
counter += 1
if counter % self.log_at == 0:
logger.info("Placed {} presents".format(counter))
logger.info("Current min z is {}".format(np.min(self.sleigh.z_map)))
logger.info("Finished placing presents")
if write:
self.write()
if check:
self.check()
return self
def perform_cross_validation(self, *args, **kwargs):
"""
Performs cross validation using the main estimator. In some cases, when we don't need to search
across a grid of hyperparameters, we may want to perform cross validation only.
"""
start_time = time.time()
if self.cv_sample is not None:
logger.info("Performing {}-fold cross validation with {:.0%} of the sample".format(self.cv_folds, self.cv_sample))
self.cv_x,\
self.cv_x_test,\
self.cv_y,\
self.cv_y_test = cross_validation.train_test_split(self.train_x, self.train_y, train_size=self.cv_sample)
else:
logger.info("Performing {}-fold cross validation with full training set".format(self.cv_folds))
self.cv_x = self.train_x
self.cv_y = self.train_y
self.cv_iterator = self.cv_class(self.cv_x.shape[0], n_folds=self.cv_folds)
params = {
'cv': self.cv_iterator,
'scoring': rmse_scorer,
'verbose': 2,
'n_jobs': self.n_jobs
}
params.update(kwargs)
# Make sure to not parallelize the estimator
if 'n_jobs' in self.estimator.get_params().keys():
self.estimator.set_params(n_jobs=1)
self.cv_scores = cross_validation.cross_val_score(self.estimator,
self.cv_x,
self.cv_y,
*args, **params)
logger.info("Cross validation completed in {}. Scores:".format(time.time() - start_time))
logger.info("{}".format(self.cv_scores))
def do_for_each_image(self, files, func, n_features, training):
"""
Function that iterates over a list of files, applying func to the image indicated by that function.
Returns an (n_samples, n_features) ndarray
"""
dims = (N_TRAIN if training else N_TEST, n_features)
predictors = np.zeros(dims)
counter = 0
for row, f in enumerate(files):
filepath = TRAIN_IMAGE_PATH if training else TEST_IMAGE_PATH
image = RawImage(os.path.join(filepath, f))
predictors[row] = func(image)
counter += 1
if counter % 1000 == 0:
logger.info("Processed {} images".format(counter))
return predictors
def build_test_predictors(self):
"""
Builds the test predictors
Returns:
None
"""
if self.test_x is None:
test_files = sorted(os.listdir(TEST_IMAGE_PATH))
if os.path.exists(self.test_predictors_file):
logger.info("Test predictors already exists, loading from file {}".format(self.test_predictors_file))
res = np.load(self.test_predictors_file)
else:
res = self.build_features(test_files, False)
logger.info("Caching test predictors to {}".format(self.test_predictors_file))
np.save(self.test_predictors_file, res)
self.test_x = res
def multi_request(request): #backend endpoint for js
logger.info(f"Multi Request Received; {request.__str__()}")
qVar1 = request.args['qVar1']
qVar2 = request.args['qVar2']
table1 = request.args['table1']
table2 = request.args['table2']
logger.debug(", ".join([qVar1, qVar2, table1, table2]))
searchVar = f'{table1}.{qVar1}, {table2}.{qVar2}'
tableName = f"{table1} INNER JOIN {table2}"
baseQ = f"SELECT * FROM {tableName} ON {table1}.{qVar1} == {table2}.{qVar2}"
query = baseQ
logger.info(query)
queryOut = get_db().execute(query).fetchall()
output = {}
output['results'] = queryOut
return jsonify(output)
def build_train_predictors(self):
"""
Builds the training predictors. Once the predictors are built, they are cached to a file.
If the file already exists, the predictors are loaded from file.
Couldn't use the @cache_to_file decorator because the decorator factory doesn't have access to self at compilation
Returns:
None
"""
if self.train_x is None:
file_list = train_solutions.filenames
if os.path.exists(self.train_predictors_file):
logger.info("Training predictors already exists, loading from file {}".format(self.train_predictors_file))
res = np.load(self.train_predictors_file)
else:
res = self.build_features(file_list, True)
logger.info("Caching training predictors to {}".format(self.train_predictors_file))
np.save(self.train_predictors_file, res)
self.train_x = res
def run(self, method, *args, **kwargs):
"""
Primary entry point for executing tasks with the model
Arguments:
----------
method: string
Must be one of 'grid_search', 'cv', 'train', or 'predict'
*args:
Additional arguments to be passed to the job
**kwargs:
Additional arguments to be passed to the job
"""
jobs = {'grid_search', 'cv', 'train', 'predict'}
if method not in jobs:
raise RuntimeError("{} is not a valid job".format(method))
start_time = time.time()
self.build_train_predictors()
res = None
if method == 'grid_search':
logger.info("Performing grid search")
res = self.perform_grid_search_and_cv(*args, **kwargs)
elif method == 'cv':
logger.info("Performing cross validation")
res = self.perform_cross_validation(*args, **kwargs)
elif method == 'train':
logger.info("Performing training")
res = self.train(*args, **kwargs)
elif method == 'predict':
logger.info("Performing prediction")
res = self.predict(*args, **kwargs)
end_time = time.time()
logger.info("Model completed in {}".format(end_time - start_time))
return res
def transform(self, X=None):
if self.training:
files = train_solutions.filenames
else:
files = sorted(os.listdir(TEST_IMAGE_PATH))
if os.path.exists(self.result_path) and not self.force_rerun:
logger.info("File already exists. Loading from {}".format(self.result_path))
if self.memmap:
return joblib.load(self.result_path, mmap_mode='r+')
else:
return joblib.load(self.result_path)
else:
res = np.vstack(Parallel(n_jobs=self.n_jobs, verbose=self.verbose)(
delayed(_parallel_crop_scale)(self, files) for files in chunks(files, self.n_jobs)
))
logger.info("Saving results to file {}".format(self.result_path))
joblib.dump(res, self.result_path)
if self.memmap:
res = joblib.load(self.result_path, mmap_mode='r+')
return res
def run(self, check=True, write=True):
layer = self.layer_class()
presents_file = os.path.join('data', self.infile)
outfile = os.path.join('data', self.outfile)
logger.info("Reading and placing presents")
counter = 0
with open(presents_file, 'rb') as presents:
presents.readline() # skip header
read = csv.reader(presents)
for row in read:
present = classes.Present(*row)
layer = self.process_present(present, layer)
counter += 1
if counter % self.log_at == 0:
logger.info("Placed {} presents".format(counter))
self.process_last_layer(layer)
logger.info("Finished placing presents")
if write:
self.write()
if check:
self.check()
return self
def kmeans_006_colwise_rmse():
crop = 150
s = 15
n_centroids = 3000
images = get_images(crop=crop, s=s)
kmeans_generator = train_kmeans_generator(images, n_centroids=n_centroids)
train_x = kmeans_generator.transform(
images,
save_to_file='data/data_kmeans_features_006_centroids_{}.npy'.format(
n_centroids),
memmap=True)
train_y = classes.train_solutions.data
train_x, test_x, train_y, test_y = train_test_split(train_x,
train_y,
train_size=0.2,
test_size=0.2)
# Unload some objects
del images
gc.collect()
wrapper = ModelWrapper(models.Ridge.RidgeRFEstimator, {
'alpha': 500,
'n_estimators': 500,
'verbose': 1
},
n_jobs=-1)
wrapper.fit(train_x, train_y)
# About 11 minutes to train the ridge regression on an m2.4 xlarge with 50% of the train set
# Took about a minute to train ridge on 0.1 of the train set, but the overall rmse was .114 compared to .106 on 50%, and .104 actual
# 5 minutes to train ridge on 0.2 of the train set, with rmse of .111
kmeans_preds = wrapper.predict(test_x)
logger.info('Kmeans')
colwise = classes.colwise_rmse(kmeans_preds, test_y)
overall = classes.rmse(kmeans_preds, test_y)
"""
def sample_top_down(infile='presents_revorder.csv', outfile='sub_topdown_1.csv', write=True, check=True):
"""
Replicate the MatLab top-down approach
Strategy is basically the same as bottom_up, but before closing each layer,
align all of the presents to the top of the layer.
Actually this strategy is not quite the same, since it reads the present in a different order.
Result is a slightly higher score than the benchmark
"""
sleigh = classes.LayerSleigh()
layer = classes.Layer()
presents_file = os.path.join('data', infile)
outfile = os.path.join('data', outfile)
logger.info("Reading and placing presents")
with open(presents_file, 'rb') as presents:
presents.readline() # skip header
read = csv.reader(presents)
for row in read:
present = classes.Present(*row)
if not layer.place_present(present):
# Can't place the present on the layer, so close the layer and start a new one
# Before closing, re-align all of the presents in the layer to the top of the layer
align_presents_to_layer_top(layer)
sleigh.add_layer(layer)
layer = classes.Layer(z=sleigh.max_z + 1)
res = layer.place_present(present)
# Add the final layer
align_presents_to_layer_top(layer)
sleigh.add_layer(layer)
if check and not sleigh.check_all():
logger.error('There is an error in the Sleigh')
return sleigh
if write:
sleigh.write_to_file(outfile)
return sleigh
def train(self, *args, **kwargs):
start_time = time.time()
logger.info("Fitting estimator")
if 'n_jobs' in self.estimator.get_params().keys():
self.estimator.set_params(n_jobs=self.n_jobs)
self.estimator.fit(self.train_x, self.train_y)
logger.info("Finished fitting model in {}".format(time.time() - start_time))
# Get an in sample RMSE
logger.info("Calculating in-sample RMSE")
self.training_predict = self.estimator.predict(self.train_x)
self.rmse = rmse(self.training_predict, self.train_y)
return self.estimator
def fit(self, X, y=None):
start_time = time.time()
logger.info("Fitting estimator")
self.estimator_ = self.get_estimator()
if 'n_jobs' in self.estimator_.get_params().keys():
self.estimator_.set_params(n_jobs=self.n_jobs)
self.estimator_.fit(X, y)
logger.info("Finished fitting model in {}".format(time.time() - start_time))
# Get an in sample RMSE
logger.info("Calculating in-sample RMSE")
self.training_predict = self.estimator_.predict(X)
self.rmse = rmse(self.training_predict, y)
def cross_validation(self, X, y, n_folds=2, cv_class=None, sample=None, parallel_estimator=False):
cls = cv_class or cross_validation.KFold
start_time = time.time()
if sample is not None:
logger.info("Performing {}-fold cross validation with {:.0%} of the sample".format(n_folds, sample))
self.cv_x,\
_,\
self.cv_y,\
_ = cross_validation.train_test_split(X, y, train_size=sample)
del _
else:
logger.info("Performing {}-fold cross validation with full training set".format(n_folds))
self.cv_x = X
self.cv_y = y
self.cv_iterator = cls(self.cv_x.shape[0], n_folds=n_folds)
params = {
'cv': self.cv_iterator,
'scoring': rmse_scorer,
'verbose': 3,
'n_jobs': self.n_jobs
}
estimator = self.get_estimator()
# Make sure to not parallelize the estimator
if 'n_jobs' in estimator.get_params().keys():
if parallel_estimator:
estimator.set_params(n_jobs=self.n_jobs)
params['n_jobs'] = 1
else:
estimator.set_params(n_jobs=1)
self.cv_scores = cross_validation.cross_val_score(estimator, self.cv_x, self.cv_y, **params)
logger.info("Cross validation completed in {}. Scores:".format(time.time() - start_time))
logger.info("{}".format(self.cv_scores))
def kmeans_006():
"""
Testing number of centroids
[(1000, array([-0.10926318, -0.10853047])),
(2000, array([-0.10727502, -0.10710292])),
(2500, array([-0.107019 , -0.10696262])),
(3000, array([-0.10713973, -0.1066932 ]))]
"""
n_centroids_vals = [1000, 2000, 2500, 3000]
scores = []
for n_centroids in n_centroids_vals:
s = 15
crop = 150
n_patches = 400000
rf_size = 5
logger.info("Training with n_centroids {}".format(n_centroids))
train_x_crop_scale = CropScaleImageTransformer(
training=True,
result_path='data/data_train_crop_{}_scale_{}.npy'.format(crop, s),
crop_size=crop,
scaled_size=s,
n_jobs=-1,
memmap=True)
test_x_crop_scale = CropScaleImageTransformer(
training=False,
result_path='data/data_test_crop_{}_scale_{}.npy'.format(crop, s),
crop_size=crop,
scaled_size=s,
n_jobs=-1,
memmap=True)
kmeans_generator = KMeansFeatureGenerator(
n_centroids=n_centroids,
rf_size=rf_size,
result_path='data/mdl_kmeans_006_centroids_{}'.format(n_centroids),
n_iterations=20,
n_jobs=-1,
)
patch_extractor = models.KMeansFeatures.PatchSampler(
n_patches=n_patches, patch_size=rf_size, n_jobs=-1)
images = train_x_crop_scale.transform()
patches = patch_extractor.transform(images)
kmeans_generator.fit(patches)
del patches
gc.collect()
train_x = kmeans_generator.transform(
images,
save_to_file='data/data_kmeans_features_006_centroids_{}.npy'.
format(n_centroids),
memmap=True)
train_y = classes.train_solutions.data
# Unload some objects
del images
gc.collect()
wrapper = ModelWrapper(models.Ridge.RidgeRFEstimator, {
'alpha': 500,
'n_estimators': 250
},
n_jobs=-1)
wrapper.cross_validation(train_x,
train_y,
n_folds=2,
parallel_estimator=True)
score = (n_centroids, wrapper.cv_scores)
logger.info("Scores: {}".format(score))
scores.append(score)
del wrapper
gc.collect()
def kmeans_006():
"""
Testing number of centroids
[(1000, array([-0.10926318, -0.10853047])),
(2000, array([-0.10727502, -0.10710292])),
(2500, array([-0.107019 , -0.10696262])),
(3000, array([-0.10713973, -0.1066932 ]))]
"""
n_centroids_vals = [1000, 2000, 2500, 3000]
scores = []
for n_centroids in n_centroids_vals:
s = 15
crop = 150
n_patches = 400000
rf_size = 5
logger.info("Training with n_centroids {}".format(n_centroids))
train_x_crop_scale = CropScaleImageTransformer(training=True,
result_path='data/data_train_crop_{}_scale_{}.npy'.format(crop, s),
crop_size=crop,
scaled_size=s,
n_jobs=-1,
memmap=True)
test_x_crop_scale = CropScaleImageTransformer(training=False,
result_path='data/data_test_crop_{}_scale_{}.npy'.format(crop, s),
crop_size=crop,
scaled_size=s,
n_jobs=-1,
memmap=True)
kmeans_generator = KMeansFeatureGenerator(n_centroids=n_centroids,
rf_size=rf_size,
result_path='data/mdl_kmeans_006_centroids_{}'.format(n_centroids),
n_iterations=20,
n_jobs=-1,)
patch_extractor = models.KMeansFeatures.PatchSampler(n_patches=n_patches,
patch_size=rf_size,
n_jobs=-1)
images = train_x_crop_scale.transform()
patches = patch_extractor.transform(images)
kmeans_generator.fit(patches)
del patches
gc.collect()
train_x = kmeans_generator.transform(images, save_to_file='data/data_kmeans_features_006_centroids_{}.npy'.format(n_centroids), memmap=True)
train_y = classes.train_solutions.data
# Unload some objects
del images
gc.collect()
wrapper = ModelWrapper(models.Ridge.RidgeRFEstimator, {'alpha': 500, 'n_estimators': 250}, n_jobs=-1)
wrapper.cross_validation(train_x, train_y, n_folds=2, parallel_estimator=True)
score = (n_centroids, wrapper.cv_scores)
logger.info("Scores: {}".format(score))
scores.append(score)
del wrapper
gc.collect()
"""
Last quoted plan benchmark
"""
import classes
from classes import logger
train = classes.get_train_data()
actuals = classes.get_actual_plan(train)
scores = []
# Score seems to be a bit high on training, about .547-.548
# Leaderboard score is 0.53793, so seems like 0.01 difference, which is pretty substantial in this competition
for n in range(5):
truncated = classes.truncate(train)
prediction = classes.get_last_observed_plan(truncated)
score = classes.score_df(prediction, actuals)
scores.append(score)
logger.info("Run {}, score: {}".format(n+1, score))
test = classes.get_test_data()
pred = classes.get_last_observed_plan(test)
classes.make_submission(pred, 'benchmark_001.csv')
from classes.logger import error, info
if __name__ == "__main__":
try:
finder = AppointmentFinder()
contacts = finder.getContactsByState()
statesUpdated = finder.getUpdatedTsByState()
for state in contacts:
cvsData = finder.getApptDataForStateCvs(state)
aptsAvailable = finder.openStateApts(cvsData)
parsedTs = finder.parseCvsTs(cvsData)
tsIsOld = True
if state in statesUpdated:
curTs = statesUpdated[state]
tsIsOld = parsedTs > curTs
if tsIsOld:
finder.updateStateTs(state, parsedTs)
statesUpdated[state] = parsedTs
info("{} appointment data timestamp updated to {}".format(
state.upper(), parsedTs))
if tsIsOld and aptsAvailable:
emails = contacts[state]
finder.sendApptAvailableEmailCvs(emails, state)
info("Appointment finder run complete!")
except Exception as e:
error(str(e))
def perform_grid_search_and_cv(self, *args, **kwargs):
"""
Performs cross validation and grid search to identify optimal parameters and to score the estimator
The grid search space is defined by self.grid_search_parameters.
If grid_search_sample is defined, then a downsample of the full train_x is used to perform the grid search
Cross validation is parallelized at the CV level, not the estimator level, because not all estimators
can be parallelized.
Parameters:
----------
refit: boolean, default True
If true, the grid search estimator is refit on the grid search set, and then is used to calculate a score
on the holdout set.
Really only useful if grid_search_sample < 1, otherwise the calculated score will basically be an in-sample
error (since the training and the testing were the same dataset)
grid_search_parameters: set on model instantiation
The grid search parameters -- should set this when you instantiate the Model, not when you call run('grid_search')
"""
if self.grid_search_parameters is not None:
logger.info("Performing grid search")
start_time = time.time()
params = {
'scoring': rmse_scorer,
'verbose': 3,
'refit': True,
'n_jobs': self.n_jobs,
'cv': 2
}
params.update(kwargs)
# Make sure to not parallelize the estimator if it can be parallelized
if 'n_jobs' in self.estimator.get_params().keys():
self.estimator.set_params(n_jobs=1)
self.grid_search_estimator = self.grid_search_class(self.estimator,
self.grid_search_parameters,
*args, **params)
if self.grid_search_sample is not None:
logger.info("Using {} of the train set for grid search".format(self.grid_search_sample))
# Downsample if a sampling rate is defined
self.grid_search_x, \
self.grid_search_x_test, \
self.grid_search_y, \
self.grid_search_y_test = cross_validation.train_test_split(self.train_x,
self.train_y,
train_size=self.grid_search_sample)
else:
logger.info("Using full train set for the grid search")
# Otherwise use the full set
self.grid_search_x = self.grid_search_x_test = self.train_x
self.grid_search_y = self.grid_search_y_test = self.train_y
self.grid_search_estimator.fit(self.grid_search_x, self.grid_search_y)
logger.info("Found best parameters:")
logger.info(self.grid_search_estimator.best_params_)
if params['refit']:
logger.info("Predicting on holdout set")
pred = self.grid_search_estimator.predict(self.grid_search_x_test)
res = rmse(self.grid_search_y_test, pred)
logger.info("RMSE on holdout set: {}".format(res))
logger.info("Grid search completed in {}".format(time.time() - start_time))
def perform_cross_validation(self, *args, **kwargs):
start_time = time.time()
if self.cv_sample is not None:
logger.info("Performing {}-fold cross validation with {:.0%} of the sample".format(self.cv_folds, self.cv_sample))
self.cv_x,\
self.cv_x_test,\
self.cv_y,\
self.cv_y_test = cross_validation.train_test_split(self.train_x, self.train_y, train_size=self.cv_sample)
else:
logger.info("Performing {}-fold cross validation with full training set".format(self.cv_folds))
self.cv_x = self.train_x
self.cv_y = self.train_y
self.cv_iterator = self.cv_class(self.cv_x.shape[0], n_folds=self.cv_folds)
params = {
'cv': self.cv_iterator,
'scoring': rmse_scorer,
'verbose': 2,
'n_jobs': self.n_jobs
}
params.update(kwargs)
# Gotta roll our own cross validation
# Cross validation will look like this:
# For each fold:
# train estimator
# Predict estimator
# Store prediction
# Move onto next estimator
overall_scores = []
detailed_scores = [{}] * self.cv_folds
for i, idx in enumerate(self.cv_iterator):
logger.debug("Working on fold {}".format(i + 1))
train = idx[0]
test = idx[1]
# Get the data
# The actual cross val method uses safe_mask to index the arrays. This is only required if
# we might be handling sparse matrices
this_train_x = self.cv_x[train]
this_train_y = self.cv_y[train]
this_test_x = self.cv_x[test]
this_test_y = self.cv_y[test]
logger.debug("Fold {} training X and Y shape: {}, {}".format(i + 1, this_train_x.shape, this_train_y.shape))
logger.debug("Fold {} test X and Y shape: {}, {}".format(i + 1, this_test_x.shape, this_test_y.shape))
test_preds = np.zeros(this_test_y.shape)
train_preds = np.zeros(this_train_y.shape)
# Should be able to refactor out this inner loop
for cls in range(1, 12):
cols = train_solutions.class_map[cls]
logger.info("Performing CV on class {}".format(cls))
# Clone the estimator
# Need to do this for each fold
estimator = clone(self.estimator[cls])
existing_test_preds = np.any(test_preds, axis=0)
existing_train_preds = np.any(train_preds, axis=0)
this_x = np.hstack((this_train_x, train_preds[:, existing_train_preds]))
test_x = np.hstack((this_test_x, test_preds[:, existing_test_preds]))
this_y = this_train_y[:, cols]
test_y = this_test_y[:, cols]
logger.debug("Train X shape: {}".format(this_x.shape))
logger.debug("Train Y shape: {}".format(this_y.shape))
logger.debug("Test X shape: {}".format(test_x.shape))
# Parallelize at the estimator level
if 'n_jobs' in estimator.get_params().keys():
estimator.set_params(n_jobs=self.n_jobs)
estimator.fit(this_x, this_y)
train_pred = estimator.predict(this_x)
test_pred = estimator.predict(test_x)
# Scale things back
if self.scaled:
# this does not work correctly because cv_y is already split
scale_factors = train_solutions.get_sum_for_class(cls)
assert train.shape[0] == scale_factors[0]
assert test.shape[0] == scale_factors[0]
train_scale_factors = scale_factors[train]
test_scale_factors = scale_factors[test]
assert train_scale_factors.shape[0] == train_pred.shape[0]
assert test_scale_factors.shape[0] == test_pred.shape[0]
train_pred = np.multiply(train_pred, train_scale_factors)
test_pred = np.multiply(test_pred, test_scale_factors)
test_y = np.multiply(test_y, test_scale_factors)
score = rmse(test_y, test_pred)
detailed_scores[i][cls] = score
logger.info("RMSE on test set for class {}: {}".format(cls, score))
train_preds[:, cols] = train_pred
test_preds[:, cols] = test_pred
if self.scaled:
pass
else:
fold_rmse = rmse(this_test_y, test_preds)
overall_scores.append(fold_rmse)
logger.info("Overall score for fold {}: {}".format(i + 1, fold_rmse))
self.cv_scores = np.array(overall_scores)
logger.info("Cross validation completed in {}. Scores:".format(time.time() - start_time))
logger.info(detailed_scores)
logger.info("Overall scores:")
logger.info(overall_scores)
from pathlib import Path
from classes.logger import error, info
if __name__ == "__main__":
try:
logFile = environ.get('LOGFILE')
if logFile:
# construct new file name, get current log directory, construct
# new file absolute path
curDate = datetime.strftime(datetime.now(), "%Y-%m-%d")
newFileName = "app.logger.{}".format(curDate)
logDir = path.dirname(logFile)
newFile = path.join(logDir, newFileName)
exist = path.isfile(newFile)
if not exist:
# if the new file doesn't already exist
# then rename the old one to the new file
Path(logFile).rename(newFile)
info("Logs successfully archived to file {}".format(newFileName))
else:
# if the file exists already don't archive
info("Log file was not archived as {} already exists.".format(newFileName))
else:
info("Unable to archive log file. No log file environment variable found.")
except Exception as e:
error(str(e))
def train(self, *args, **kwargs):
start_time = time.time()
logger.info("Fitting estimator")
preds = np.zeros(self.train_y.shape)
# This currently just goes from 1 to 11, but the tree doesn't actually progress in that order.
# Maybe experiment with a more fine-grained control over which predictions get passed in
for cls in range(1, 12):
cols = train_solutions.class_map[cls]
# Select the correct estimator, and get the right subsets of the data to use in training
logger.info("Fitting estimator for class {}".format(cls))
estimator = self.estimator[cls]
existing_preds = np.any(preds, axis=0) # Boolean array of which columns are populated in preds
# X is concatenated with any predictions that have already been made
logger.debug("Adding columns {} of predictions to X".format(np.where(existing_preds)[0]))
this_x = np.hstack((self.train_x, preds[:, existing_preds]))
this_y = self.train_y[:, cols]
logger.debug("X is of shape {}".format(this_x.shape))
logger.debug("Y is of shape {}".format(this_y.shape))
# Train the current estimator
if 'n_jobs' in estimator.get_params().keys():
estimator.set_params(n_jobs=self.n_jobs)
estimator.fit(this_x, this_y)
# Make predictions with the current estimator, and store those predictions
logger.info("Making predictions for class {}".format(cls))
y_pred = estimator.predict(this_x)
logger.debug("Ypred is of shape {}".format(this_y.shape))
logger.info("RMSE of class {} is {}".format(cls, rmse(y_pred, this_y)))
preds[:, cols] = y_pred
logger.info("Finished fitting model in {}".format(time.time() - start_time))
# Get an in sample RMSE
logger.info("Calculating overall in-sample RMSE")
self.training_predict = preds
self.rmse = rmse(self.training_predict, self.train_y)
return self.estimator
def predict(self, X):
if not hasattr(self, 'estimator_'):
raise RuntimeError("Estimator has not been trained")
logger.info("Predicting")
return self.estimator_.predict(X)
import os
from classes import logger
import csv
import classes
infile = 'presents_short.csv'
layer = classes.Layer()
presents_file = os.path.join('data', infile)
logger.info("Reading and placing presents")
with open(presents_file, 'rb') as presents:
presents.readline() # skip header
read = csv.reader(presents)
for row in read:
present = classes.Present(*row)
if not layer.place_present(present):
break
areas = []
presents_file = os.path.join('data', infile)
logger.info("Reading and placing presents")
with open(presents_file, 'rb') as presents:
presents.readline() # skip header
read = csv.reader(presents)
for row in read:
present = classes.Present(*row)
areas.append((present.pid, present.x * present.y))
import math
def grid_search(self, X, y, grid_search_params, grid_search_class=None, sample=None, n_folds=2, refit=True, parallel_estimator=False):
cls = grid_search_class or grid_search.GridSearchCV
logger.info("Performing grid search")
start_time = time.time()
params = {
'scoring': rmse_scorer,
'verbose': 3,
'refit': refit,
'n_jobs': self.n_jobs,
'cv': n_folds
}
estimator = self.get_estimator()
if 'n_jobs' in estimator.get_params().keys():
# If the estimator can be parallelized, and parallel_estimator is True, then parallelize at that level
# otherwise parallelize at the grid search level
if parallel_estimator:
estimator.set_params(n_jobs=self.n_jobs)
params['n_jobs'] = 1
else:
estimator.set_params(n_jobs=1)
self.grid_search_estimator = cls(estimator, grid_search_params, **params)
if sample is not None:
logger.info("Using {} of the train set for grid search".format(sample))
# Downsample if a sampling rate is defined
self.grid_search_x, \
self.grid_search_x_test, \
self.grid_search_y, \
self.grid_search_y_test = cross_validation.train_test_split(X,
y,
train_size=sample)
else:
logger.info("Using full train set for the grid search")
# Otherwise use the full set
self.grid_search_x = self.grid_search_x_test = X
self.grid_search_y = self.grid_search_y_test = y
self.grid_search_estimator.fit(self.grid_search_x, self.grid_search_y)
logger.info("Found best parameters:")
logger.info(self.grid_search_estimator.best_params_)
logger.info("All results:")
logger.info(pprint.pformat(self.grid_search_estimator.grid_scores_))
if params['refit']:
logger.info("Predicting on holdout set")
pred = self.grid_search_estimator.predict(self.grid_search_x_test)
res = rmse(self.grid_search_y_test, pred)
logger.info("RMSE on holdout set: {}".format(res))
logger.info("Grid search completed in {}".format(time.time() - start_time))