def load_train_and_test(self, train, test):
if isinstance(train, pd.DataFrame) and isinstance(test, pd.DataFrame):
return train, test
trainextension, testextension = get_extension(train.basename()), get_extension(test.basename())
trainloadf, testloadf = getattr(pd, 'read_' + trainextension), getattr(pd, 'read_' + testextension)
train: pd.DataFrame = trainloadf(train)
test: pd.DataFrame = testloadf(test)
return train, test
def process_methods(self, diff_only=False, changes=[]):
"""
Main method that documents methods in a file. To any
file that needs to be documented. Process methods is the
entry point for getting the whole thing done
Parameters
----------
bool diff_only: Use a diff only. Consumed by dyc diff.
list changes: Changes in a file, mainly use also with dyc diff.
"""
print('\nProcessing Methods\n\r')
for filename in self.file_list:
try:
change = filter(lambda x: x.get('path') == filename,
changes)[0]
except:
change = None
extension = get_extension(filename)
fmt = self.formats.get(extension)
method_cnf = fmt.get('method', {})
method_cnf['arguments'] = fmt.get('arguments')
builder = MethodBuilder(filename, method_cnf)
builder.initialize(change=change)
builder.prompts()
builder.apply()
builder.clear(filename)
def check_news(item):
'''check_news(item):
Performs convalidation on the data loaded from load_news() and raises
ValueError if something is wrong.
'''
if not item['title']:
raise ValueError(u'Impossibile caricare una notizia senza titolo')
if not item['content']:
raise ValueError(u'Impossibile caricare una notizia senza testo')
# datepick_to_datetime() itself will raise the ValueError in case
item['date'] = datepick_to_datetime(item['date'])
for p in item['photos']:
if re.match('^image/[A-Za-z]*', p[1].mimetype) and p[0] == '': # If I have a photo without the label
raise ValueError( u"Impossibile caricare foto senza una descrizione." )
# It is possible to UPDATE the label of an existing photo (so a pair label-nophoto is allowed),
# while it is impossible to load a photo without a label, because the label is always rendered in the page
# and thus loaded with the photo. In case of UPLOAD I must check again and raise errors for every unpaired label.
if not allowed_pic(p[1].filename):
raise ValueError( u'''{0} non può essere caricato:<br>
'*.{1}' non è tra le estensioni ammesse (ovvero {2}).<br>
Ricarica le foto.
'''.format(p[1].filename, get_extension(p[1].filename), set_to_string(ALLOWED_EXTENSIONS_PICS)) )
# Secondary issue: now the user have to reload all the photos.
# It is possible to let him see again what they loaded, and correct?
return
def parse_json(self,data):
ipdata = json.loads(data)
try:
if ipdata['imgs']:
for n in ipdata['imgs']: #data子项
if n['objURL']:
try:
proxy_support = urllib2.ProxyHandler(proxy)
opener = urllib2.build_opener(proxy_support)
urllib2.install_opener(opener)
#print "proxy",proxy
self.lock()
self.dbcurr.execute('select ID from pic_info where objURL=%s', (n['objURL']))
y = self.dbcurr.fetchone()
#print "y=",y
if y:
print "database exist"
self.unlock() #continue 前解锁
continue
else:
real_extension=utils.get_extension(n['objURL'])
req = urllib2.Request(n['objURL'],headers=i_headers)
resp = urllib2.urlopen(req,None,5)
dataimg=resp.read()
name=str(uuid.uuid1())
filename=""
if len(real_extension)>4:
real_extension=".gif"
real_extension=real_extension.lower()
if real_extension==".gif":
filename =self.makeDateFolder("E://sosogif", "d"+str(self.count % 60))+"//"+name+"-www.sosogif.com-搜搜gif贡献"+real_extension
self.count+=1
else:
filename =self.makeDateFolder("E://sosogif", "o"+str(self.count % 20))+"//"+name+"-www.sosogif.com-搜搜gif贡献"+real_extension
self.count+=1
"""
name=str(uuid.uuid1())
filename=""
if len(real_extension)>4:
real_extension=".gif"
filename =self.makeDateFolder("E://sosogif", "d"+str(self.count % 60))+"//"+name+"-www.sosogif.com-搜搜gif贡献"+real_extension
self.count+=1
"""
try:
if not os.path.exists(filename):
file_object = open(filename,'w+b')
file_object.write(dataimg)
file_object.close()
self.anaylis_info(n,filename,real_extension) #入库操作
else:
print "file exist"
except IOError,e1:
print "e1=",e1
pass
self.unlock()
except IOError,e2:
#print "e2=",e2
pass
self.chance1+=1
def context_iter(self, context=None):
"""
Iterate the tree depth-first, producing a context for each node.
Args:
context (dict): The parent context object
Yields:
dict: The context object for this node
"""
if not context:
context = {'parent_container_type': None}
# Depth-first walk down tree
context['container_type'] = self.type
context[self.type] = self
# Bring subject to top-level of context
if self.type == 'session':
context['subject'] = self.data['subject']
# Additionally bring ext up if file
if self.type == 'file':
context['ext'] = utils.get_extension(self.data['name'])
# Yield the current context before processing children
yield context
context['parent_container_type'] = self.type
for child in self.children:
context_copy = context.copy()
for ctx in child.context_iter(context_copy):
yield ctx
def remove_unique_indicators(path):
print path
for filename in os.listdir(path):
if ' (2)' in filename:
index = filename.index(' (2)')
extension = utils.get_extension(filename, with_dot=True)
shorter_filename = filename[:index] + extension
print filename
os.rename(os.path.join(path, filename), os.path.join(path, shorter_filename))
def find_train_test():
where_train = Question("Where is your train dataset under project root?",
'data/raw/train.csv')
where_test = Question("Where is your test dataset under project root?",
'data/raw/test.csv')
train_path = where_train.ask()
test_path = where_test.ask()
is_csv = get_extension(train_path) == 'csv'
if is_csv:
what_sep = Question('Specify separator into csv file:', ',')
csv_sep = what_sep.ask()
train, test = pd.read_csv(train_path,
csv_sep), pd.read_csv(test_path, csv_sep)
else:
load_f = getattr(pd, 'read_' + get_extension(train_path))
train = load_f(train_path)
load_f = getattr(pd, 'read_' + get_extension(test_path))
test = load_f(test_path)
return train, test
def main():
parser = argparse.ArgumentParser(description='Generate average atlas for an image folder.')
parser.add_argument('--in_folder', type=str,
help='The input image folder')
parser.add_argument('--out', type=str,
help='The output image path (with .nii.gz)')
parser.add_argument('--ref', type=str,
help='Path of reference image. Define the affine and header of output nii.gz')
parser.add_argument('--num_processes', type=int, default=20)
args = parser.parse_args()
file_list_all = os.listdir(args.in_folder)
print('Process images under folder: ', args.in_folder)
print('Number of files in folder %s is %d' % (args.in_folder, len(file_list_all)))
nifti_file_list = [file_path for file_path in file_list_all if get_extension(file_path) == '.gz']
print('Number of nii.gz files: ', len(nifti_file_list))
file_name_chunks = get_chunks_list(nifti_file_list, args.num_processes)
pool = Pool(processes=args.num_processes)
result_list = [pool.apply_async(average_nii_file_list_mem, (file_name_chunk, args.in_folder)) for file_name_chunk in file_name_chunks]
# Get the shape.
# im_temp = nib.load(os.path.join(args.in_folder, nifti_file_list[0]))
im_temp = nib.load(args.ref)
im_header = im_temp.header
im_affine = im_temp.affine
im_temp_data = im_temp.get_data()
im_shape = im_temp_data.shape
averaged_image = np.zeros(im_shape)
for thread_idx in range(len(result_list)):
result = result_list[thread_idx]
result.wait()
print(f'Thread with idx {thread_idx} / {len(result_list)} is completed')
print('Adding to averaged_image...')
averaged_image_chunk = result.get()
chunk_size = len(file_name_chunks[thread_idx])
averaged_image = np.add(averaged_image, np.multiply(averaged_image_chunk, chunk_size))
print('Done.')
print('')
print('Averaging over all images...')
averaged_image = np.divide(averaged_image, len(nifti_file_list))
print('Done.')
print('Output to file: ', args.out)
averaged_image_obj = nib.Nifti1Image(averaged_image, affine=im_affine, header=im_header)
nib.save(averaged_image_obj, args.out)
def sort_files(path, filetype='gif'):
"""
Sort files into a specific folder while *not* maintaining existing
file structure patterns.
"""
target_dir = "_{}s".format(filetype.lower())
target = os.path.join(path, target_dir)
for root, dirnames, filenames in os.walk(path):
for filename in filenames:
if ".ds_store" in filename.lower():
continue
extension = utils.get_extension(filename).strip('.')
if extension == filetype.lower():
utils.make_dir(target)
new_name = utils.find_untaken_name(filename, target)
os.rename(os.path.join(root, filename), os.path.join(target, new_name))
def get_target_file_path(url, file_title, subreddit_target_dir, subfolder=None, new_only=False):
file_extension = utils.get_extension(url)
"""
if not utils.has_acceptable_extension(url):
print "Not an accepted extension."
continue
"""
file_title = u"{}.{}".format(file_title, file_extension)
clean_file_title = strip_rank_from_title(file_title)
file_path = os.path.join(subreddit_target_dir, file_title)
if subfolder:
dir_path = os.path.join(subreddit_target_dir, subfolder)
file_path = os.path.join(dir_path, file_title)
make_dirs(dir_path)
if os.path.isfile(file_path):
print u"\"{}\" already exists.".format(file_title)
return False
print "Pulling {} ...".format(url),
return file_path
def process(host, path, callback):
path, workers = _build_workers(path)
source_file = get_file(host + path)
if get_extension(path) == 'svg':
# http://redmine.pearbox.net/issues/1605
source_image_type = 'svg+xml'
else:
image = get_image(source_file)
exif = image.info.get('exif', b'')
source_image_type = image.format.upper()
for worker in workers:
#extract palette from Image
pl = image.getpalette()
image = worker.do(image)
if pl is not None:
#if image has palette then restore it
image.putpalette(pl)
source_file = StringIO()
image.save(source_file, source_image_type, exif=exif)
data = source_file.getvalue()
data_len = len(data)
logging.info(
'Image was successful processed with type {type} and len {data_len}'.
format(type=source_image_type, data_len=data_len))
callback('200 OK',
[('Content-type', 'image/{type}'.format(type=source_image_type)),
('Content-length', str(data_len))])
return [data]
async def create_meme_tempfile(imgpath, text, text_top=None):
ext = utils.get_extension(imgpath)
temp = tempfile.NamedTemporaryFile(suffix=f".{ext}", delete=False)
await create_meme(imgpath, temp.name, text, text_top)
return temp.name
def parse_json(self, data):
ipdata = json.loads(data)
try:
if ipdata['imgs']:
for n in ipdata['imgs']: #data子项
if n['objURL']:
try:
proxy_support = urllib2.ProxyHandler(proxy)
opener = urllib2.build_opener(proxy_support)
urllib2.install_opener(opener)
#print "proxy",proxy
self.lock()
self.dbcurr.execute(
'select ID from pic_info where objURL=%s',
(n['objURL']))
y = self.dbcurr.fetchone()
#print "y=",y
if y:
print "database exist"
self.unlock() #continue 前解锁
continue
else:
real_extension = utils.get_extension(
n['objURL'])
req = urllib2.Request(n['objURL'],
headers=i_headers)
resp = urllib2.urlopen(req, None, 5)
dataimg = resp.read()
name = str(uuid.uuid1())
filename = ""
if len(real_extension) > 4:
real_extension = ".gif"
real_extension = real_extension.lower()
if real_extension == ".gif":
filename = self.makeDateFolder(
"E://sosogif",
"d" + str(self.count % 60)
) + "//" + name + "-www.sosogif.com-搜搜gif贡献" + real_extension
self.count += 1
else:
filename = self.makeDateFolder(
"E://sosogif",
"o" + str(self.count % 20)
) + "//" + name + "-www.sosogif.com-搜搜gif贡献" + real_extension
self.count += 1
"""
name=str(uuid.uuid1())
filename=""
if len(real_extension)>4:
real_extension=".gif"
filename =self.makeDateFolder("E://sosogif", "d"+str(self.count % 60))+"//"+name+"-www.sosogif.com-搜搜gif贡献"+real_extension
self.count+=1
"""
try:
if not os.path.exists(filename):
file_object = open(filename, 'w+b')
file_object.write(dataimg)
file_object.close()
self.anaylis_info(
n, filename, real_extension) #入库操作
else:
print "file exist"
except IOError, e1:
print "e1=", e1
pass
self.unlock()
except IOError, e2:
#print "e2=",e2
pass
self.chance1 += 1
def update_news(request, cursor, app, id):
'''update_news(request, cursor, app, id):
This function updates a news, meaning that it can identify and
overwrite a specific row in the database. Basically the same as the
above for the text parts, but slightly different concerning the
management of pictures.
NB: it DOESN'T DEAL with the ValueErrors. The caller is supposed to
manage them.
'''
item = load_news(request)
check_news(item)
old_pics = retrieve_item("news", id, cursor)['pics']
try:
for n in xrange(len(item['photos'])):
if old_pics[n][1] != item['photos'][n][0]: # If labels are different, update them
old_pics[n][1] = item['photos'][n][0]
if item['photos'][n][1].filename != '': # If I have a new file:
# Save it
filename = 'File{0}.{1}'.format(str(datetime.datetime.now()).translate(None, '.:- ')[:-3], get_extension(secure_filename(item['photos'][n][1].filename)))
item['photos'][n][1].save(os.path.join(app.config['UPLOAD_FOLDER_PICS'], filename))
# Delete the old one
try:
os.remove(os.path.join(BASE_PATH, app.config['UPLOAD_FOLDER_PICS'], old_pics[n][2]))
except OSError as e:
# If the file there isn't, I simply leave the corrupted one (if exists) orphan.
app.logger.error('OSError occurred in update_NEWS, probly orphan file. Error Code: {0}'.format(e))
# Overwrite te name of the file in the database entry
old_pics[n][2] = filename
except IndexError: # Means that I'm trying to update one more photo, than what I have in old_pics (I'm adding a photo)
filename = 'File{0}.{1}'.format(str(datetime.datetime.now()).translate(None, '.:- ')[:-3], get_extension(secure_filename(item['photos'][n][1].filename)))
item['photos'][n][1].save(os.path.join(app.config['UPLOAD_FOLDER_PICS'], filename))
old_pics.append( (n, item['photos'][n][0], filename) )
item['pics'] = old_pics
cursor.execute("UPDATE news SET data=?, title=?, text=?, pics=? WHERE id = ?", [item['date'], item['title'], item['content'], json.dumps(item['pics']), id])
return item
def upload_doc(request, cursor, app):
'''upload_doc(request, cursor, app):
This function performs a fresh upload of all the data previously
loaded and checked.
It adds a new row in the database without overwriting anything.
In case of failure, it returns all the non-checked raw loaded data,
to be displayed again to the user and let they correct it.
NB: it DOESN'T DEAL with the ValueErrors. The caller is supposed to
manage them.
'''
item = load_doc(request)
check_doc(item)
filename = 'File{0}.{1}'.format(str(datetime.datetime.now()).translate(None, '.:- ')[:-3], get_extension(secure_filename(item['file'].filename)))
item['file'].save(os.path.join(app.config['UPLOAD_FOLDER_DOCS'], filename))
cursor.execute("INSERT INTO docs (name, path) VALUES (?, ?)", [item['title'], filename])
return
from datetime import datetime
from collections import defaultdict
from bokeh.plotting import figure
from bokeh.io import export_svgs
from multiprocessing import Pool
def date_to_month(d):
return datetime(d.year, d.month, 1)
base_dir = "/home/visgean/Dropbox/**/*"
picture_extensions = ['.jpg', '.jpeg', '.png']
pictures = list(filter(
lambda f: utils.get_extension(f) in picture_extensions,
glob.iglob(base_dir, recursive=True)
))
with Pool(12) as p:
exif_data = p.map(utils.get_exif, pictures)
dates = p.map(utils.parse_date, exif_data)
filesize_counter = defaultdict(int)
image_counter = defaultdict(int)
for filename, date in dates:
if not date:
continue
month = date_to_month(date)
def update_doc(request, cursor, app, id):
'''update_doc(request, cursor, app, id):
This function updates a document, meaning that it can identify and
overwrite a specific row in the database.
NB #1: It doesn't call check_doc(), because the user may want to change
only the label, without replacing the original file, and reverse.
NB #2: it doesn't deal with the ValueErrors. The caller is supposed to
manage them.
'''
item = load_doc(request)
if item['file']:
old_file = retrieve_item('doc', id, cursor)
# First of all I upload the new file
filename = 'File{0}.{1}'.format(str(datetime.datetime.now()).translate(None, '.:- ')[:-3], get_extension(secure_filename(item['file'].filename)))
item['file'].save(os.path.join(app.config['UPLOAD_FOLDER_DOCS'], filename))
cursor.execute("UPDATE docs SET path=? WHERE id = ?", [json.dumps(filename), id])
#Then I remove the old one
try:
os.remove(os.path.join(BASE_PATH, app.config['UPLOAD_FOLDER_DOCS'], old_file['path']))
except OSError as e:
# If the file there isn't, I simply leave the corrupted one (if exists) orphan.
app.logger.error('OSError in update_DOC, probly orphan file. Error Code: {0}'.format(e))
if item['title']:
cursor.execute("UPDATE docs SET name=? WHERE id = ?", [item['title'], id])
else:
raise ValueError(u'''Impossibile caricare un documento senza titolo.<br>
Se il titolo non è stato caricato automaticamente, contatta il webmaster.''')
return item
def upload_news(request, cursor, app):
'''upload_news(request, cursor, app):
This function performs a fresh upload of all the material previously
loaded and checked (except for the unvalidation of unpaired labels,
that is allowed for the uploading, but not allowed here.)
It adds a new row in the database without overwriting anything.
In case of failure, it returns all the non-checked raw loaded data,
to be displayed again to the user and let they correct it.
NB: it DOESN'T DEAL with the ValueErrors. The caller is supposed to
manage them.
'''
item = load_news(request)
check_news(item)
# Validation
for l in item['photos']:
if (not re.match('^image/[A-Za-z]*', l[1].mimetype) ) and l[0]!= None:
raise ValueError( u"Impossibile caricare una descrizione senza la relativa foto." )
paths, labels = [], []
for f in item['photos']:
filename = 'File{0}.{1}'.format(str(datetime.datetime.now()).translate(None, '.:- ')[:-3], get_extension(secure_filename(f[1].filename)))
f[1].save(os.path.join(app.config['UPLOAD_FOLDER_PICS'], filename))
paths.append(filename)
labels.append(f[0])
pics = zip(xrange(len(paths)), labels, paths)
cursor.execute("INSERT INTO news (data, title, text, pics) VALUES (?, ?, ?, ?)", [item['date'], item['title'], item['content'], json.dumps(pics)])
return
def main():
# Parse arguments from command line
parser = argparse.ArgumentParser(
description='Anonymize a dataset using Mondrian in Spark.')
parser.add_argument('METADATA', help='json file that describes the job.')
parser.add_argument('WORKERS',
default=4,
type=int,
help='Number of initial cuts (workers)')
parser.add_argument('DEMO',
default=0,
type=int,
help='Start tool in demo mode')
parser.add_argument('TEST',
default=0,
type=int,
help='Start tool in test mode')
args = parser.parse_args()
demo = args.DEMO
test = args.TEST
start_time = time.time()
with open(args.METADATA) as fp:
job = json.load(fp)
# Create Spark Session
spark = SparkSession \
.builder \
.appName('mondrian') \
.getOrCreate()
spark.sparkContext.setLogLevel("WARN")
# Enable Arrow-based columnar data transfers
spark.conf.set('spark.sql.execution.arrow.pyspark.enabled', 'true')
if demo == 1:
print("\n[*] Spark context initialized")
print("\tWait for 10 seconds to continue demo...")
time.sleep(10)
# Parameters
filename_in = job['input']
filename_out = job['output']
# when repartition is not given it defaults to repartitionByRange
if 'repartition' in job and \
job['repartition'] in {'customRepartition',
'repartitionByRange',
'noRepartition'}:
repartition = job['repartition']
else:
repartition = 'repartitionByRange'
id_columns = job.get('id_columns', [])
redact = job.get('redact', False)
quasiid_columns = job['quasiid_columns']
sensitive_columns = job.get('sensitive_columns')
# when column score is not given it defaults to span
score_functions = {
'span': span,
'entropy': entropy,
'neg_entropy': neg_entropy
}
if 'column_score' in job and job['column_score'] in score_functions:
column_score = score_functions[job['column_score']]
else:
column_score = span
fragments = min(args.WORKERS, job.get('max_fragments', 10**6))
K = job.get('K')
L = job.get('L')
measures = job.get('measures', [])
# Setup mondrian_fragmentation function
mondrian = functools.partial(mondrian_fragmentation,
sensitive_columns=sensitive_columns,
is_valid=get_validation_function(K, L))
# when fraction is not given it defaults to None
if 'fraction' in job and 0 < job['fraction'] < 1:
fraction = job['fraction']
else:
fraction = None
# when fragmentation is not given it defaults to quantile_fragmentation
fragmentation_functions = {
'mondrian': mondrian,
'quantile': quantile_fragmentation
}
if 'fragmentation' in job and \
job['fragmentation'] in fragmentation_functions:
fragmentation = fragmentation_functions[job['fragmentation']]
else:
fragmentation = quantile_fragmentation
if not K and not L:
raise Exception("Both K and L parameters not given or equal to zero.")
if L and not sensitive_columns:
raise Exception(
"l-diversity needs to know which columns are sensitive.")
if fraction and fragmentation == mondrian:
sys.exit('''Sorry, currently mondrian fregmentation criteria is only
available without sampling.''')
if demo == 1:
print("\n[*] Job details initialized")
print("\tWait for 10 seconds to continue demo...")
time.sleep(10)
print('\n[*] Using {} initial partitions\n'.format(fragments))
# Read file according to extension
print('[*] Reading from {}\n'.format(filename_in))
extension = get_extension(filename_in)
df = spark.read \
.options(header='true', inferSchema='true') \
.format(extension).load(filename_in)
if fraction:
df = df.sample(fraction=fraction)
pdf = df.toPandas()
pdf.info()
print('\n[*] Fragmentation details\n')
"""
TODO: Avoid having a single node performing this step for the whole dataset
"""
if not fraction:
# Create first cut
pdf = create_fragments(df=pdf,
quasiid_columns=quasiid_columns,
column_score=column_score,
fragments=fragments,
colname='fragment',
criteria=fragmentation)
# Check first cut
sizes = pdf.groupby('fragment').size()
print("\n[*] Dataset distribution among fragments\n")
print(sizes)
print("\n[*] Dataset with fragmentation info\n")
print(pdf.head)
# Compute the range on the quasi-identifiers columns
# will be useful for information loss evaluation
quasiid_range = [-1] * len(quasiid_columns)
for i, column in enumerate(quasiid_columns):
quasiid_range[i] = span(pdf[column])
# Recreate the dataframe in a way that is appreciated by pyarrow.
pdf = pd.DataFrame.from_dict(pdf.to_dict())
# Create spark dataframe
df = spark.createDataFrame(pdf)
else:
# Compute quantiles on the sample
column, bins = get_fragments_quantiles(df=pdf,
quasiid_columns=quasiid_columns,
column_score=column_score,
fragments=fragments)
# Read entire file in distributed manner
df = spark.read \
.options(header='true', inferSchema='true').csv(filename_in)
bins[0] = float(
"-inf") # to prevent out of Bucketizer bounds exception
bins[-1] = float(
"inf") # to prevent out of Bucketizer bounds exception
if len(bins) != 2:
# split into buckets only if there are more than 1
bucketizer = Bucketizer(splits=bins,
inputCol=column,
outputCol='fragment')
df = bucketizer.transform(df)
else:
# otherwise assign every row to bucket 0
df = df.withColumn('fragment', F.lit(0.0))
# Check first cut
sizes = df.groupBy('fragment').count()
print("\n[*] Dataset distribution among fragments\n")
sizes.show()
print("\n[*] Dataset with fragmentation info\n")
df.show()
# Compute the range on the quasi-identifiers columns
# will be useful for information loss evaluation
categoricals = [
item[0] for item in df.dtypes
if item[0] in quasiid_columns and item[1].startswith('string')
]
funcs = (F.countDistinct(F.col(cname)) if cname in categoricals else
F.max(F.col(cname)) - F.min(F.col(cname))
for cname in quasiid_columns)
quasiid_range = df.agg(*funcs).collect()[0]
# Create a schema in which identifiers are either not there or strings
# and quasi identifiers are strings.
# This is needed because the result of the UDF has to generalize them.
if not redact:
schema = T.StructType(
df.select([
column for column in df.columns if column not in id_columns
]).schema)
else:
schema = T.StructType(df.schema)
for column in id_columns:
schema[column].dataType = T.StringType()
for column in quasiid_columns:
schema[column].dataType = T.StringType()
# TODO: add a column to the output schema to keep information on the
# equivalent classes to avoid reconstructing them from scratch
# in the evaluation of the metrics
if demo == 1 and fragments > 1:
print("\n[*] Dataset fragmented")
print("\tWait for 10 seconds to continue demo...")
time.sleep(10)
# initialize taxonomies
quasiid_gnrlz = __generalization_preproc(job, df, spark=spark)
if demo == 1 and quasiid_gnrlz:
print("\n[*] Taxonomies data preprocessed")
print("\tWait for 10 seconds to continue demo...")
time.sleep(10)
# Create the pandas udf
@F.pandas_udf(schema, F.PandasUDFType.GROUPED_MAP)
def anonymize_udf(pdf):
adf = anonymize(df=pdf,
id_columns=id_columns,
redact=redact,
quasiid_columns=quasiid_columns,
sensitive_columns=sensitive_columns,
column_score=column_score,
K=K,
L=L,
quasiid_gnrlz=quasiid_gnrlz)
# Ensure that the quasi identifier columns have been converted
# to strings (they are required by the return type).
for column in quasiid_columns:
adf[column] = adf[column].astype('object')
return adf
if repartition == 'repartitionByRange':
df = df.repartitionByRange('fragment')
elif repartition == 'customRepartition':
df = repartition_dataframe(df, spark)
print('\n[*] Starting anonymizing the dataframe\n')
print('Number of DF partitions: {}'.format(df.rdd.getNumPartitions()))
''' Debug spark partitioning -> Low performance
count = 0
for elem in df.rdd.glom().collect():
print("Size of Spark Partition {}: {}".format(count, len(elem)))
count +=1
'''
adf = df \
.groupby('fragment') \
.applyInPandas(anonymize_udf.func, schema=anonymize_udf.returnType) \
.cache()
# Create Discernability Penalty udf
schema = T.StructType(
[T.StructField('information_loss', T.LongType(), nullable=False)])
@F.pandas_udf(schema, F.PandasUDFType.GROUPED_MAP)
def discernability_penalty_udf(adf):
dp = discernability_penalty(adf=adf, quasiid_columns=quasiid_columns)
# pandas_udf requires a pandas dataframe as output
return pd.DataFrame({'information_loss': [dp]})
# Create Normalized Certainty Penalty udf
schema = T.StructType(
[T.StructField('information_loss', T.DoubleType(), nullable=False)])
@F.pandas_udf(schema, F.PandasUDFType.GROUPED_MAP)
def normalized_certainty_penalty_udf(adf):
gcp = normalized_certainty_penalty(adf=adf,
quasiid_columns=quasiid_columns,
quasiid_range=quasiid_range,
quasiid_gnrlz=quasiid_gnrlz)
# pandas_udf requires a pandas dataframe as output
return pd.DataFrame({'information_loss': [gcp]})
if repartition == 'repartitionByRange':
adf = adf.repartitionByRange('fragment')
elif repartition == 'customRepartition':
adf = repartition_dataframe(adf, spark)
print('Number of ADF partitions: {}'.format(adf.rdd.getNumPartitions()))
adf.drop('fragment').show(10)
print('\n[*] Anonymized dataframe')
if demo == 1:
print("\tWait for 10 seconds to continue demo...\n")
time.sleep(10)
# dictionary to store test params
measures_log = {}
measures_log["fragments"] = fragments
measures_log["repartition"] = repartition
measures_log["K"] = K
measures_log["L"] = L
measures_log["fraction"] = fraction
if measures:
print('[*] Information loss evaluation\n')
for measure in measures:
if measure == 'discernability_penalty':
dp = evaluate_information_loss(adf, discernability_penalty_udf)
print(f"Discernability Penalty = {dp:.2E}")
measures_log["DP"] = dp
elif measure == 'normalized_certainty_penalty':
ncp = evaluate_information_loss(adf,
normalized_certainty_penalty_udf)
print(f"Normalized Certainty Penalty = {ncp:.2E}")
measures_log["NCP"] = ncp
elif measure == 'global_certainty_penalty':
gcp = evaluate_information_loss(adf,
normalized_certainty_penalty_udf)
gcp /= (len(quasiid_columns) * adf.count())
print(f"Global Certainty Penalty = {gcp:.4f}")
measures_log["GCP"] = gcp
# Remove fragmentation information
adf = adf.drop('fragment')
# Write file according to extension
print(f"\n[*] Writing to {filename_out}\n")
extension = get_extension(filename_out)
adf.write \
.mode("overwrite") \
.options(header=True) \
.format(extension) \
.save(filename_out)
end_time = time.time()
execution_time = end_time - start_time
measures_log["timestamp"] = end_time
measures_log["time"] = execution_time
if test == 1:
# Write test params to Hadoop
test_result_files = [
"hdfs://namenode:8020/anonymized/test_results.csv",
"hdfs://namenode:8020/anonymized/artifact_result.csv"
]
print("[*] Creating test configuration file on Hadoop")
write_test_params(spark, measures_log, test_result_files)
if demo == 0:
print("--- %s seconds ---" % (execution_time))
spark.stop()
print('\n[*] Done\n')
def startSpiderWap(self):
if self.spider_queue.empty():
fetched_users = self.db.execute(
'SELECT * from spider_list ORDER BY weight DESC limit 0,30')
if fetched_users <= 0:
print 'nothing to spider,spider_list is empty'
return False
self.start = 'start'
self.errno = ERR_NO
fetchall = self.db.fetchall()
# 将数据库中取出的待爬取的分享者，加入爬取队列
for item in fetchall:
self.spider_queue.put({
'sid': item[0],
'uk': item[1],
'file_fetched': item[2],
'follow_fetched': item[3],
'follow_done': item[4],
'file_done': item[5],
'weight': item[6],
'uid': item[7]
})
self.got_follow_count = 0
self.got_files_count = 0
self.while_count = 0
while not self.spider_queue.empty():
self.while_count += 1
share_user = self.spider_queue.get()
# 爬取分享者的文件列表
if not share_user['file_done']:
print '%d now spidering file ,%d file fetched' % (
share_user['uk'], share_user['file_fetched'])
rs = self.getShareListsWap(share_user['uk'],
share_user['file_fetched'])
if not rs:
print 'uk:%d error to fetch files,try again later...' % share_user[
'uk']
return True
total_count, fetched_count, file_list = rs
total_fetched = share_user['file_fetched'] + fetched_count
print 'fetched_file_count:%d' % fetched_count
if total_fetched >= total_count or total_count == 0:
share_user['file_done'] = 1 # 该分享者所有文件爬取完成
if total_count == 0:
self.db.execute(
"UPDATE spider_list set file_done=%s WHERE sid=%s",
(1, share_user['sid']))
self.db.commit()
else:
try:
files_count = 0
for file in file_list:
files_count += 1
ext = ''
file_type = ''
file_type_i = -1
if file['isdir'] == 0 and file[
'feed_type'] == 'share':
ext = utils.get_extension(
file['title']).lower()
file_type = utils.get_category(ext)
file_type_i = self.file_type_t[file_type]
time_stamp = int(time.time())
self.db.execute(
"INSERT INTO share_file (title,uk,shareid,shorturl,isdir,size,md5,ext,feed_time,create_time,file_type,uid,feed_type) VALUES(%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s)",
(file['title'], file['uk'], file['shareid'],
file['shorturl'], file['isdir'], file['size'],
file['md5'], ext, file['feed_time'],
time_stamp, file_type_i, share_user['uid'],
file['feed_type']))
except:
share_user['file_done'] = 0
self.db.rollback()
traceback.print_exc()
return False
else:
self.db.execute(
"UPDATE spider_list set file_fetched=%s,file_done=%s WHERE sid=%s",
(total_fetched, share_user['file_done'],
share_user['sid']))
self.db.execute(
"UPDATE share_users set fetched=%s WHERE uid=%s",
(total_fetched, share_user['uid']))
share_user['file_fetched'] = total_fetched
self.got_files_count += files_count
self.db.commit()
# 爬取完文件后在爬取订阅列表，wap暂时不爬取
if share_user['follow_done'] == 0 and share_user['file_done'] == 1:
share_user['follow_done'] = 1
print '删除用户:%d' % share_user['sid']
self.db.execute("DELETE FROM spider_list WHERE sid=%s",
(share_user['sid'], ))
self.db.commit()
time.sleep(SPIDER_INTERVAL)
print '-----------------Done------------------'
print 'while_count:%d' % self.while_count
print 'got_follow_count:%d' % self.got_follow_count
print 'got_files_count:%d' % self.got_files_count
return True
print("Directory " + folderName + " already exists")
if not os.path.exists(fileFolderName):
os.mkdir(fileFolderName)
print("Directory " + fileFolderName + " Created ")
else:
print("Directory " + fileFolderName + " already exists")
i = 0
for doc_id in doc_id_list:
url_final = url_descarga_1 + doc_id + url_descarga_2
file_path = os.path.join(
fileFolderName, date_name + "&" + number_list[i] + "&" + entry_number_list[i])
print("\n" + file_path)
file_extension = utils.get_extension(url_final)
file_complete_path = file_path + "." + file_extension
if os.path.exists(file_complete_path):
os.remove(file_complete_path)
file_name = wget.download(url_final, file_complete_path)
if (file_extension != "pdf"):
utils.convert_to_pdf(file_name)
i = i + 1
input("\nPress any key to close")
def main():
parser = argparse.ArgumentParser(description='Generate average atlas for an image folder.')
parser.add_argument('--in_folder', type=str,
help='The input image folder')
parser.add_argument('--out_union', type=str,
help='The output image path (with .nii.gz)')
parser.add_argument('--out_inter', type=str,
help='The output image path (with .nii.gz)', default='')
parser.add_argument('--ref', type=str,
help='Path of reference image. Define the affine and header of output nii.gz')
parser.add_argument('--num_processes', type=int, default=10)
args = parser.parse_args()
file_list_all = os.listdir(args.in_folder)
print('Process images under folder: ', args.in_folder)
print('Number of files in folder %s is %d' % (args.in_folder, len(file_list_all)))
nifti_file_list = [file_path for file_path in file_list_all if get_extension(file_path) == '.gz']
print('Number of nii.gz files: ', len(nifti_file_list))
file_name_chunks = get_chunks_list(nifti_file_list, args.num_processes)
pool = Pool(processes=args.num_processes)
# Get the shape.
# im_temp = nib.load(os.path.join(args.in_folder, nifti_file_list[0]))
im_temp = nib.load(args.ref)
im_header = im_temp.header
im_affine = im_temp.affine
im_temp_data = im_temp.get_data()
im_shape = im_temp_data.shape
averaged_image_union = np.zeros(im_shape)
averaged_image_inter = np.zeros(im_shape)
averaged_image_union.fill(np.nan)
# averaged_image_inter.fill(np.nan)
non_null_mask_count_image = np.zeros(im_shape)
if args.out_inter != '':
print('Average in intersection:')
image_average_inter_result_list = [pool.apply_async(sum_images_inter,
(file_name_chunk, args.in_folder))
for file_name_chunk in file_name_chunks]
for thread_idx in range(len(image_average_inter_result_list)):
result = image_average_inter_result_list[thread_idx]
result.wait()
print(f'Thread with idx {thread_idx} / {len(image_average_inter_result_list)} is completed')
print('Adding to averaged_image...')
averaged_image_chunk = result.get()
averaged_image_inter = add_image_inter(averaged_image_inter, averaged_image_chunk)
print('Done.')
averaged_image_inter = np.divide(averaged_image_inter,
len(nifti_file_list),
out=averaged_image_inter,
where=np.logical_not(np.isnan(averaged_image_inter)))
average_image_inter_obj = nib.Nifti1Image(averaged_image_inter, affine=im_affine, header=im_header)
print(f'Saving to {args.out_inter}')
nib.save(average_image_inter_obj, args.out_inter)
print('Done.')
print('')
print('Average in union')
image_average_union_result_list = [pool.apply_async(sum_images_union,
(file_name_chunk, args.in_folder))
for file_name_chunk in file_name_chunks]
for thread_idx in range(len(image_average_union_result_list)):
result = image_average_union_result_list[thread_idx]
result.wait()
print(f'Thread with idx {thread_idx} / {len(image_average_union_result_list)} is completed')
print('Adding to averaged_image...')
averaged_image_chunk = result.get()
averaged_image_union = add_image_union(averaged_image_union, averaged_image_chunk)
print('Done.')
non_null_mask_count_result = [pool.apply_async(sum_non_null_count,
(file_name_chunk, args.in_folder))
for file_name_chunk in file_name_chunks]
for thread_idx in range(len(non_null_mask_count_result)):
result = non_null_mask_count_result[thread_idx]
result.wait()
print(f'Thread with idx {thread_idx} / {len(non_null_mask_count_result)} is completed')
print('Adding to averaged_image...')
averaged_image_chunk = result.get()
non_null_mask_count_image = np.add(non_null_mask_count_image, averaged_image_chunk)
print('Done.')
averaged_image_union = np.divide(averaged_image_union,
non_null_mask_count_image,
out=averaged_image_union,
where=non_null_mask_count_image>0)
averaged_image_union_obj = nib.Nifti1Image(averaged_image_union, affine=im_affine, header=im_header)
nib.save(averaged_image_union_obj, args.out_union)
print('Done.')
def fetch_spacex_last_launch():
images = get_spacex_last_launch_images()
for image_number, image_url in enumerate(images):
download_file(
image_url, 'spacex{}.{}'.format(image_number,
get_extension(image_url)))
def startSpider(self):
if self.spider_queue.empty():
fetched_users = self.db.execute('SELECT * from spider_list ORDER BY weight DESC limit 0,20')
if fetched_users <= 0:
print('nothing to spider,spider_list is empty')
return False
self.start = 'start'
self.errno = ERR_NO
fetchall = self.db.fetchall()
# 将数据库中取出的待爬取的分享者，加入爬取队列
for item in fetchall:
self.spider_queue.put({
'sid': item[0],
'uk': item[1],
'file_fetched': item[2],
'follow_fetched': item[3],
'follow_done': item[4],
'file_done': item[5],
'weight': item[6],
'uid': item[7]
})
self.got_follow_count = 0
self.got_files_count = 0
self.while_count = 0
while not self.spider_queue.empty():
self.while_count += 1
share_user = self.spider_queue.get()
# 爬取分享者的文件列表
if not share_user['file_done']:
print('%d now spidering file ,%d file fetched' % (share_user['uk'], share_user['file_fetched']))
rs = self.getShareLists(share_user['uk'], share_user['file_fetched'])
if not rs:
print('uk:%d error to fetch files,try again later...' % share_user['uk'])
return True
total_count, fetched_count, file_list = rs
total_fetched = share_user['file_fetched'] + fetched_count
print('fetched_file_count:%d' % fetched_count)
if total_fetched >= total_count or total_count == 0:
share_user['file_done'] = 1 # 该分享者所有文件爬取完成
if total_count == 0:
self.db.execute("UPDATE spider_list set file_done=%s WHERE sid=%s", (1, share_user['sid']))
self.db.commit()
else:
try:
files_count = 0
for file in file_list:
files_count += 1
ext = ''
file_type = ''
file_type_i = -1
if file['isdir'] == 0 and file['feed_type'] == 'share':
ext = utils.get_extension(file['title']).lower()
file_type = utils.get_category(ext)
file_type_i = self.file_type_t[file_type]
time_stamp = int(time.time())
self.db.execute(
"INSERT INTO share_file (title,uk,shareid,shorturl,isdir,size,md5,ext,feed_time,create_time,file_type,uid,feed_type) VALUES(%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s)",
(file['title'], file['uk'], file['shareid'],
file['shorturl'], file['isdir'], file['size'], file['md5'], ext, file['feed_time'],
time_stamp, file_type_i, share_user['uid'], file['feed_type'])
)
except:
share_user['file_done'] = 0
self.db.rollback()
traceback.print_exc()
return False
else:
self.db.execute("UPDATE spider_list set file_fetched=%s,file_done=%s WHERE sid=%s",
(total_fetched, share_user['file_done'], share_user['sid']))
self.db.execute("UPDATE share_users set fetched=%s WHERE uid=%s",
(total_fetched, share_user['uid']))
share_user['file_fetched'] = total_fetched
self.got_files_count += files_count
self.db.commit()
# 爬取完文件后在爬取订阅列表
if share_user['follow_done'] == 0 and share_user['file_done'] == 1:
print('%d now spidering follow ,%d follow fetched' % (share_user['uk'], share_user['follow_fetched']))
rs = self.getFollows(share_user['uk'], share_user['follow_fetched'])
if not rs:
print('error to fetch follows,try again later...')
return
total_count, fetched_count, follow_list = rs
total_fetched = share_user['follow_fetched'] + fetched_count
print('fetched_follow_count:%d' % fetched_count)
if total_fetched >= total_count or total_count == 0:
share_user['follow_done'] = 1
if total_count == 0:
self.db.execute("DELETE FROM spider_list WHERE sid=%s", (share_user['sid'],))
self.db.commit()
else:
try:
follow_count = 0
for follow in follow_list:
follow_count += 1
# 判断该用户是否已经在表中了
if self.db.execute('SELECT * FROM share_users WHERE uk=%s', (follow['follow_uk'],)) > 0:
print('uk:%d has already in share_user table' % follow['follow_uk'])
continue
time_stamp = int(time.time())
self.db.execute("INSERT INTO share_users (uk,user_name,avatar_url,intro,follow_count,album_count,\
fens_count,pubshare_count,last_visited,create_time,weight) VALUES(%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s)",
(
follow['follow_uk'], follow['follow_uname'], follow['avatar_url'],
follow['intro'], follow['follow_count'],
follow['album_count'], follow['fans_count'], follow['pubshare_count'],
time_stamp, time_stamp, 5
)
)
# 将获取的新分享者加入爬取列表
self.db.execute("INSERT INTO spider_list (uk,uid) VALUES(%s,%s)",
(follow['follow_uk'], self.db.last_row_id()))
except:
share_user['follow_done'] = 0
self.db.rollback()
traceback.print_exc()
return False
else:
if share_user['follow_done'] == 1:
# 订阅者爬取完成，该分享者的任务完成，从待爬取列表中删除
print('delete follow fetched sid:%d from spider_list' % share_user['sid'])
self.db.execute("DELETE FROM spider_list WHERE sid=%s", (share_user['sid'],))
else:
self.db.execute("UPDATE spider_list set follow_fetched=%s,follow_done=%s WHERE sid=%s",
(total_fetched, share_user['follow_done'], share_user['sid']))
share_user['follow_fetched'] = total_fetched
self.got_follow_count += follow_count
self.db.commit()
# 只要分享者列表没完成，说明该分享者还未爬取完，则加入工作队列，继续爬取
if share_user['follow_done'] == 0:
self.spider_queue.put(share_user)
else:
print('%d has done' % share_user['uk'])
del share_user
time.sleep(SPIDER_INTERVAL)
print('-----------------Done------------------')
print('while_count:%d' % self.while_count)
print('got_follow_count:%d' % self.got_follow_count)
print('got_files_count:%d' % self.got_files_count)
return True
np.save(without_extension(_file) + '.npy', encoding)
print("(batch_size, time_steps, dimensions) :", encoding.shape)
# plotting #
if PLOT:
fig, axs = plt.subplots(2, 1, figsize=(10, 5))
axs[0].plot(audio)
axs[0].set_title('Audio Signal')
axs[1].plot(encoding[0])
axs[1].set_title('NSynth Encoding')
# decoding #
'''Synthesizes audio from the encoding and saves it'''
fastgen.synthesize(
encoding,
save_paths=[without_extension(_file) + "_decoded." + get_extension(_file)],
samples_per_save=sample_length)
if DEBUG:
print("Generation for normal encoding achieved !")
# slower and faster encoding #
encoding_slower = timestretch(encoding, 1.5)
encoding_faster = timestretch(encoding, 0.5)
if PLOT:
fig, axs = plt.subplots(3, 1, figsize=(10, 7), sharex=True, sharey=True)
axs[0].plot(encoding[0])
axs[0].set_title('Encoding (Normal Speed)')
axs[1].plot(encoding_faster[0])
axs[1].set_title('Encoding (Faster))')
